[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/19775034/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/19780561/transformed.cor.cli.txt"

nPatients in clinical file=412, in cluster file=408, common to both=408
[1]  82 408
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               90               318 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               90               318 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              128               280 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              128               280 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              111               297 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              111               297 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               57               351 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               57               351 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              142               266 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              142               266 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              178               230 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              178               230 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               38               370 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               38               370 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               26               382 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               26               382 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              166               242 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              166               242 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               53               355 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               53               355 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               78               330 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               78               330 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               41               367 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               41               367 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              171               237 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              171               237 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              150               258 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              150               258 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               90               318 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               90               318 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              203               205 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              203               205 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               68               340 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               68               340 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               56               352 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               56               352 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               116                292 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               116                292 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                45                363 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                45                363 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                28                380 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                28                380 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                48                360 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                48                360 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               115                293 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               115                293 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                92                316 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                92                316 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               100                308 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               100                308 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                58                350 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                58                350 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                35                373 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                35                373 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                74                334 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                74                334 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                83                325 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                83                325 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                58                350 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                58                350 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               136                272 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               136                272 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               117                291 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               117                291 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                63                345 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                63                345 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                87                321 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                87                321 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               134                274 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               134                274 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               201                207 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               201                207 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               229                179 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               229                179 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               115                293 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               115                293 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                49                359 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                49                359 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               66               342 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               66               342 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               47               361 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               47               361 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34               374 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34               374 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               34               374 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               34               374 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               45               363 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               45               363 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               91               317 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               91               317 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               53               355 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               53               355 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               24               384 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               24               384 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              143               265 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              143               265 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              136               272 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              136               272 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               56               352 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               56               352 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              159               249 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              159               249 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              100               308 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              100               308 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              159               249 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              159               249 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               21               387 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               21               387 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               27               381 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               27               381 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              188               220 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              188               220 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               38               370 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               38               370 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              175               233 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              175               233 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              170               238 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              170               238 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                74                334 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                74                334 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               128                280 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               128                280 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               181                227 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               181                227 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               131                277 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               131                277 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                56                352 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                56                352 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                60                348 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                60                348 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                86                322 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                86                322 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               122                286 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               122                286 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               145                263 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               145                263 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               107                301 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               107                301 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               103                305 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               103                305 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               180                228 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               180                228 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                43                365 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                43                365 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                99                309 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                99                309 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               146                262 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               146                262 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                94                314 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                94                314 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                57                351 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                57                351 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                33                375 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                33                375 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                14                394 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                14                394 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                79                329 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                79                329 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               159                249 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               159                249 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               71               337 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               71               337 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               80               328 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               80               328 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 408 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=158,	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=269,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'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 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'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 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 408 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "NUMBER_PACK_YEARS_SMOKED"    "NUMBER_OF_LYMPH_NODES"      
[11] "RACE"                        "ETHNICITY"                  
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
  1   3 119 195  58 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
     123      195       58 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   3 119 195  58 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
     123      195       58 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
235  47  75   9 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
235  47  75   9 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
235  47  75   9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
235  47  75   9 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, 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=21, 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    48  42
  1P GAIN WILD-TYPE 181 135
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               90               316 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               42               135 
$`1P GAIN MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A3PJ 
      104.65        10.22        47.80         5.06        17.16        12.82 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A3MI TCGA-CU-A0YN TCGA-CU-A5W6 TCGA-DK-A2I1 
        8.98         1.94        12.16        12.92         1.84        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU 
        7.79       142.78        13.58         8.15         8.22        23.21 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U 
       17.98        64.18        38.24        15.02       166.03        19.00 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A97Q 
       11.18        20.32        38.83        25.58         0.56         8.09 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SO TCGA-FD-A3SR 
        8.94         4.01        60.66        24.30         5.52        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A5C0 TCGA-FD-A6TG TCGA-FD-A6TI 
       12.85         7.56        19.33        18.08         3.06         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3BM 
       31.07        17.23         3.25        20.12        29.36        21.40 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A3OS TCGA-GD-A76B 
       15.81        19.13        24.92         0.49        20.98         7.36 
TCGA-GU-A42P TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A6ZA 
       10.92        14.27        19.82        20.28        36.49        22.72 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        9.07        11.70        11.80        15.32        15.58        13.48 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HD 
       38.99        22.68         3.02        29.56         6.21        97.45 
TCGA-XF-A9SG TCGA-XF-A9SU TCGA-XF-A9T5 TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAMZ 
       48.62         5.98        66.64         2.96        98.99        44.32 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9RE TCGA-ZF-A9RN 
       86.30        18.15        13.64        21.86         3.48        20.22 
TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       19.69        63.02        56.35        35.41        54.21        19.17 

$`1P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97        94.88       108.95         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 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       29.65         2.50        17.42        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        26.14 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK 
        8.35         8.25        16.18        20.48         4.67         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        28.70        36.43        28.41        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S 
       12.56        13.97        12.59        12.13        13.08        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-A9FL 
       12.00        12.10        11.34        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08         4.90        15.12        18.48         5.19        29.79 
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 
       46.68        87.32         4.80        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       163.30        66.05        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M 
       76.60        67.36        15.68        50.70        36.66        52.01 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       165.73        18.81        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 
       56.15        12.03        43.59        15.35        29.72         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       22.16         2.24        16.70         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
        4.24        24.03        24.66         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-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04        12.62        22.52        27.98        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       29.16        25.74        46.78        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV 
        3.62        15.58        26.73        53.88        11.01         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.69         8.25        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-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.36         2.27         4.31        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94        11.08        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       59.31        33.01         7.23        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 
       70.32        20.71        15.91        14.07        17.75         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       13.91         7.73         2.10         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       18.97         7.63        32.78        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       10.65        32.98         7.00        21.34        19.10         8.48 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       27.35         8.58        19.07         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       64.01         9.01        12.16        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.76         9.14        27.68        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R 
       16.27        52.73        50.56        35.97        46.98        44.38 
TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        1.15        21.07        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O 
       16.54        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 
       78.25        69.34       112.83         3.91        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       51.32        45.04         6.58       125.49        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.87        17.88        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       66.41        34.45        14.93         4.21        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-AAMG 
       16.27         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-AAMW 
       11.31        54.90         7.63        71.57        91.73         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 
        6.77        56.48        30.94        61.45        27.06        75.39 
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        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
       25.41        21.11        31.20        30.28        35.84        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       94.29        13.41        64.08        58.72        88.87        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 
        2.89        34.06         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        12.23 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.49              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           166.03            165.73 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            18.03             16.77 
[1] "0.5 - 166.0 (18.0)" "0.1 - 165.7 (16.8)"
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         0       26        28       36
  1P GAIN WILD-TYPE       2      103       112       99
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               26               103
  STAGE III              28               112
  STAGE IV               36                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
  1P GAIN MUTATED         23  45  14
  1P GAIN WILD-TYPE      100 150  44
D1V4, multiclass
          clus
vv         1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1+T2              23               100
  T3                    45               150
  T4                    14                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
  1P GAIN MUTATED    43  15  17   5
  1P GAIN WILD-TYPE 192  32  58   4
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              43               192
  N1              15                32
  N2              17                58
  N3               5                 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"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    40   1
  1P GAIN WILD-TYPE 152  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     40    1
  1P GAIN WILD-TYPE  152   10
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              40               152
  1               1                10
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    26  64
  1P GAIN WILD-TYPE  81 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     26   64
  1P GAIN WILD-TYPE   81  237
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              26                81
  MALE                64               237
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    79   3
  1P GAIN WILD-TYPE 285  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     79    3
  1P GAIN WILD-TYPE  285   16
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               79               285
  YES               3                16
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, continuous
D1V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       4                         5    75
  1P GAIN WILD-TYPE    39                        17   252
D1V12, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   4                39
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                  75               252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2  83
  1P GAIN WILD-TYPE   7 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   83
  1P GAIN WILD-TYPE    7  286
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              83               286
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    71  57
  1Q GAIN WILD-TYPE 158 120
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              128               278 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               57               120 
$`1Q GAIN MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 
       11.97       104.65        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-A3MI TCGA-CF-A47V TCGA-CF-A8HY TCGA-CF-A9FF 
        8.98         1.94        12.16        12.46        11.34        11.87 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AD 
       18.58        12.92        18.48         1.84        21.86       112.44 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X2 
       17.95         7.79        13.58         8.15         8.22        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T 
       64.18        67.36        38.24        15.02       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        13.64        20.32        38.83        29.72         0.10 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B7 
       25.58         0.66        13.68         8.09         8.94         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SR 
       60.66        24.30        23.41        17.98         5.52        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BU TCGA-FD-A5C0 TCGA-FD-A5C1 
       12.85         7.56         3.62        19.33        18.08        58.92 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-AA3F TCGA-GC-A3BM 
        3.06         9.67        10.65         3.25        29.36        21.40 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A2C5 
       15.81        19.13        17.75        24.92         0.49         7.73 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-AATO TCGA-GV-A3JV 
        2.10        20.98         7.36        10.92        10.65        14.27 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.10        19.82        36.49        22.72        38.60        64.01 
TCGA-K4-A3WS TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-KQ-A41N 
       25.02         9.07        11.70        17.72        11.80        52.73 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HD 
       38.99        22.68         3.02        29.56         6.21        97.45 
TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SU 
       15.35        17.88        48.62         3.22        15.98         5.98 
TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       11.90        66.64         2.96        98.99        44.32        56.48 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9RC 
       86.30        18.15         0.66        13.64        21.86        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RN TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       13.41         3.48        20.22        63.02        56.35        35.41 
TCGA-ZF-AA58 TCGA-ZF-AA5H 
       54.21        19.17 

$`1Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       24.13        94.88       108.95         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        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
        0.62        66.54        15.12        29.65         2.50        17.42 
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        26.14        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-A3PH 
       14.89        14.96         8.35         8.25        16.18         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR 
       12.82         9.96        17.56        36.43        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S 
       12.56        13.97        12.59        12.13        13.08        10.95 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
       12.10        11.34        13.08         4.90        15.12         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       29.79        13.58         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       16.70       130.88        16.14        17.62        15.62        46.68 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
      142.78        87.32         4.80        17.72        50.27        21.30 
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       163.30        66.05 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M 
       53.29        76.60        15.68        50.70        36.66        52.01 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA75 
       13.58       165.73        13.64        15.35        56.15        11.18 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       12.03        43.59        15.35        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        0.92         1.22        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77        33.04        12.62        22.52        27.98 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       29.16        25.74        46.78        27.35        14.96        20.91 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX 
       15.58        26.73        53.88        11.01         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        8.25        27.45         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-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
        4.31        10.85        31.07        12.66        17.23         8.94 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       11.08        61.94        48.00        15.95        26.93        59.31 
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-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       70.32        20.71        15.91        14.07         8.94        13.91 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        3.12         2.20        11.31        18.97         7.63        32.78 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW 
       20.05         5.62         4.73        32.98         7.00        21.34 
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-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       19.40         9.01        12.16         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41O 
        9.14        27.68         1.81        15.42        16.27        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       35.97        46.98        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 
       16.54        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 
       78.25        69.34       112.83         3.91        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
       51.32        45.04         6.58       125.49        97.12         1.87 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       64.80        79.66        66.41        34.45        14.93         4.21 
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-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 
        8.32         6.77        30.94        61.45        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        3.88        18.84         9.63        11.97        22.36        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RF 
       21.11        31.20        30.28        35.84        28.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       58.72        88.87        47.84         2.89        34.06        19.69 
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        12.23 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.10              0.56 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           166.03            165.73 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           17.915            16.770 
[1] "0.1 - 166.0 (17.9)" "0.6 - 165.7 (16.8)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         0       38        37       52
  1Q GAIN WILD-TYPE       2       91       103       83
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               38                91
  STAGE III              37               103
  STAGE IV               52                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
  1Q GAIN MUTATED         36  62  19
  1Q GAIN WILD-TYPE       87 133  39
D2V4, multiclass
          clus
vv         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1+T2              36                87
  T3                    62               133
  T4                    19                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
  1Q GAIN MUTATED    63  18  29   5
  1Q GAIN WILD-TYPE 172  29  46   4
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              63               172
  N1              18                29
  N2              29                46
  N3               5                 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"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    56   5
  1Q GAIN WILD-TYPE 136   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     56    5
  1Q GAIN WILD-TYPE  136    6
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              56               136
  1               5                 6
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    35  93
  1Q GAIN WILD-TYPE  72 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     35   93
  1Q GAIN WILD-TYPE   72  208
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              35                72
  MALE                93               208
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   108   7
  1Q GAIN WILD-TYPE 256  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    108    7
  1Q GAIN WILD-TYPE  256   12
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              108               256
  YES               7                12
[1] 2 2
[1] FALSE
D2V9, continuous
D2V10, continuous
D2V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       9                         8   103
  1Q GAIN WILD-TYPE    34                        14   224
D2V12, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN               8                14
  WHITE                                 103               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"
D2V13, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2 115
  1Q GAIN WILD-TYPE   7 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2  115
  1Q GAIN WILD-TYPE    7  254
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO             115               254
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    62  49
  2P GAIN WILD-TYPE 167 128
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              111               295 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               49               128 
$`2P GAIN MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-5N-A9KM 
       16.77         0.62        41.75        51.16        15.12        17.42 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB 
       12.39        13.15        19.04         5.06         8.35        16.18 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
       20.48        12.82        28.70        28.41         8.98        23.01 
TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A8HY TCGA-CU-A0YR TCGA-DK-A1A3 
       12.56        12.13        12.62        11.34        15.12        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 
       66.41        18.41       130.88       112.44        17.95         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A3X2 
       87.32         4.80         8.15         8.22        66.05        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        36.66        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA76 
      166.03        18.81        19.00        13.64        11.18        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A97Q TCGA-FD-A3NA 
       20.32        43.59        25.58        24.03         8.09        60.66 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A62O 
       46.78        19.79        27.35        20.91        27.45         7.10 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A3EE 
       12.36         2.27         3.06         4.31        17.23         3.25 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       11.08        17.62        14.07        13.91         7.73         2.10 
TCGA-GD-A3OS TCGA-GU-A764 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3QF TCGA-GV-A3QH 
       20.98        20.05        32.98         7.00        20.28         8.48 
TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI 
       27.35        19.40        38.60        25.02        21.24        11.70 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-UY-A78K 
        1.81        15.42        50.56        35.97        44.38        17.62 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HD 
       22.68        69.34       112.83        29.56         6.21        97.45 
TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-AAMG TCGA-XF-AAMZ TCGA-ZF-A9R0 
       15.35        15.98        14.93       110.60        44.32        22.36 
TCGA-ZF-A9R3 TCGA-ZF-A9RC TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V 
       31.20        94.29        20.22        34.06        19.69        59.38 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       56.35        19.40         8.52 

$`2P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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-5N-A9KI 
       50.04        66.54        10.22        47.80        29.65         2.50 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20N 
       40.08         7.33         2.66         6.74         6.58        26.14 
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-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16         4.67         9.96        17.56        36.43 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI 
        1.94        12.79        13.97        12.59        13.08        12.16 
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-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.00        12.10        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90        18.48         5.19        29.79         1.84 
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-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS 
       15.62        46.68       142.78        13.58        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       163.30 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R 
       53.29        76.60        50.70        52.01        13.58       165.73 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       15.35        13.64        56.15        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.96        26.24         4.24        24.66         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-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-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
       25.74        12.85         7.56        14.96         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-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S 
        8.25        18.08        58.92         2.70         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FD-A6TK 
       62.86        18.81         6.15        12.69         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ 
       31.07        12.66        10.65         8.94        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        59.31        33.01         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        70.32        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       15.81        19.13        15.91        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        8.94         3.12         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       18.97         7.63        32.78         5.62         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E 
       14.27        21.34        19.10        19.82        36.49         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07        22.72         1.51        64.01         9.01        12.16 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ 
        3.45         2.76         9.14        27.68         9.07        17.72 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R 
       16.27        11.80        52.73        46.98         1.15        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-A78L TCGA-UY-A78N 
        1.84        16.54        12.43        38.99        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       76.01        78.25         3.02         3.91        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
       51.32        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-A9SM TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       34.45         4.21         5.98        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-AAMH 
       66.64         2.10        13.74        92.98        10.82        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-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        6.77        98.99        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        18.15         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        25.41        21.11        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       35.84        21.86        28.41        13.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       58.72        88.87        47.84         2.89         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       63.02        35.41        57.90        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.62              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           166.03            165.73 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            19.04             16.27 
[1] "0.6 - 166.0 (19.0)" "0.1 - 165.7 (16.3)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED         0       31        32       47
  2P GAIN WILD-TYPE       2       98       108       88
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               31                98
  STAGE III              32               108
  STAGE IV               47                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
  2P GAIN MUTATED         31  54  14
  2P GAIN WILD-TYPE       92 141  44
D3V4, multiclass
          clus
vv         2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1+T2              31                92
  T3                    54               141
  T4                    14                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
  2P GAIN MUTATED    51  16  28   4
  2P GAIN WILD-TYPE 184  31  47   5
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              51               184
  N1              16                31
  N2              28                47
  N3               4                 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    51   5
  2P GAIN WILD-TYPE 141   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     51    5
  2P GAIN WILD-TYPE  141    6
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              51               141
  1               5                 6
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    39  72
  2P GAIN WILD-TYPE  68 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     39   72
  2P GAIN WILD-TYPE   68  229
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              39                68
  MALE                72               229
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    95   5
  2P GAIN WILD-TYPE 269  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     95    5
  2P GAIN WILD-TYPE  269   14
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               95               269
  YES               5                14
[1] 2 2
[1] FALSE
D3V9, continuous
D3V10, continuous
D3V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       8                         6    93
  2P GAIN WILD-TYPE    35                        16   234
D3V12, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   8                35
  BLACK OR AFRICAN AMERICAN               6                16
  WHITE                                  93               234
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     3  96
  2P GAIN WILD-TYPE   6 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   96
  2P GAIN WILD-TYPE    6  273
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO              96               273
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    32  25
  2Q GAIN WILD-TYPE 197 152
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               57               349 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               25               152 
$`2Q GAIN MUTATED`
TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-5N-A9KM TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A2LB 
       51.16        15.12        17.42        12.39        19.04        16.18 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-CF-A3MG TCGA-CF-A8HY TCGA-CF-A9FF 
       17.56        28.70        28.41        12.13        11.34        11.87 
TCGA-CU-A0YR TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 
       15.12        66.41       130.88       112.44        17.95         7.79 
TCGA-DK-A3IN TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA75 
        8.22        38.24        15.02        19.00        13.64        11.18 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A62O TCGA-FD-A6TG 
       12.03        43.59        60.66        46.78         7.10         3.06 
TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GD-A3OS TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3QF 
       17.23        17.62        20.98        32.98         7.00        20.28 
TCGA-GV-A3QH TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV 
        8.48        19.07        19.40        64.01        25.02        21.24 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41O TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OD 
       11.70         1.81        50.56        17.62        22.68       112.83 
TCGA-UY-A9PB TCGA-XF-A8HD TCGA-XF-A9SK TCGA-ZF-A9R0 TCGA-ZF-A9RC TCGA-ZF-AA4R 
       29.56        97.45        15.98        22.36        94.29        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA51 TCGA-ZF-AA56 
       19.69        56.35         8.52 

$`2Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04         0.62        41.75        66.54        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80        29.65         2.50        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        26.14        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-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        17.16        20.48         4.67        12.82         9.96 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       36.43         8.98         1.94        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       13.97        12.59        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.10        11.34        18.58        13.08        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       18.48         5.19        29.79         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
        2.14        18.41        19.00        16.70        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        46.68       142.78        87.32         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.15        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       163.30        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6X 
       52.01        13.58       165.73       166.03        18.81        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        56.15        20.32        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
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-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-A3SR TCGA-FD-A3SS 
       17.98        29.16         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 
        7.56        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-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        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        11.08        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        59.31        33.01         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       66.02         6.94        70.32        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81        19.13        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-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
       32.78        20.05         5.62         4.73        10.65        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       21.34        19.10        19.82        36.49        27.35         8.58 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       22.72         1.51        38.60         9.01        12.16         3.45 
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        17.72        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R 
       16.27        11.80        52.73        35.97        46.98        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        1.15        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        16.54        12.43        38.99 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        86.83        76.01        78.25        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
        3.91        17.82         6.21         3.85        51.32        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-A9SM 
       48.62        64.80        79.66         3.22        66.41        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       14.93         4.21         5.98        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        18.15         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        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        31.20        30.28        35.84        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        64.08        58.72        88.87        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        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  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 
            19.04             16.67 
[1] "1.8 - 130.9 (19.0)" "0.1 - 166.0 (16.7)"
[1] "hr=" "1.2"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED         0       18        17       22
  2Q GAIN WILD-TYPE       2      111       123      113
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               18               111
  STAGE III              17               123
  STAGE IV               22               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
  2Q GAIN MUTATED         17  24   6
  2Q GAIN WILD-TYPE      106 171  52
D4V4, multiclass
          clus
vv         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1+T2              17               106
  T3                    24               171
  T4                     6                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
  2Q GAIN MUTATED    30   9  11   1
  2Q GAIN WILD-TYPE 205  38  64   8
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              30               205
  N1               9                38
  N2              11                64
  N3               1                 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"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    23   2
  2Q GAIN WILD-TYPE 169   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     23    2
  2Q GAIN WILD-TYPE  169    9
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              23               169
  1               2                 9
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    18  39
  2Q GAIN WILD-TYPE  89 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     18   39
  2Q GAIN WILD-TYPE   89  262
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              18                89
  MALE                39               262
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    53   1
  2Q GAIN WILD-TYPE 311  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     53    1
  2Q GAIN WILD-TYPE  311   18
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               53               311
  YES               1                18
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, continuous
D4V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       5                         3    47
  2Q GAIN WILD-TYPE    38                        19   280
D4V12, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   5                38
  BLACK OR AFRICAN AMERICAN               3                19
  WHITE                                  47               280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     1  49
  2Q GAIN WILD-TYPE   8 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   49
  2Q GAIN WILD-TYPE    8  320
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              49               320
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    76  65
  3P GAIN WILD-TYPE 153 112
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              141               265 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               65               112 
$`3P GAIN MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA84 
       24.13        16.27        16.77        34.98        27.62        15.12 
TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20J 
       47.80        17.42         7.33         6.74        12.39        19.04 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-CF-A1HR TCGA-CF-A3MF 
        8.35        20.48         4.67         9.96        12.79        12.59 
TCGA-CF-A3MG TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       12.13         4.90        15.12        29.79         1.84        21.86 
TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IN 
        2.14       112.44        46.68        17.95        87.32         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6S 
       50.27        23.21        17.98        64.18        36.66       166.03 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ 
       19.00        13.64        13.64        12.03        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW 
       38.83         0.10         0.56         4.24        24.03        13.68 
TCGA-E7-A97Q TCGA-FD-A43U TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TE 
        8.09        20.91        18.08         7.10         6.28        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.27         3.06         4.31         9.67        10.65        17.23 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES 
        3.25        11.08        61.94        48.00        59.31        33.01 
TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GC-A6I3 
       17.62        29.36        20.71        15.81         0.49        13.91 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-AATO 
        2.10        20.98         7.36        10.92         7.63        10.65 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        7.00        14.27        21.34        20.28         8.48        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS 
       19.07        22.72        19.40        38.60         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41O 
        3.45        21.24         9.07        15.42        11.80        50.56 
TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
       35.97        44.38         1.15        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        38.99        17.62        37.05        86.83        69.34 
TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HF 
        3.02        29.56        17.82        51.32         6.58        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SU 
       15.35         1.87        17.88        48.62        79.66         5.98 
TCGA-XF-A9SV TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAMY 
       12.76        13.74        10.82         7.63         6.77        98.99 
TCGA-XF-AAMZ TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RM 
       44.32        22.36        30.28        94.29        13.41        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89        19.69        59.38        63.02        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       57.90        19.40        54.21 

$`3P GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       11.97        94.88       104.65       108.95         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        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J 
       66.54        10.22        29.65         2.50        40.08         2.66 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        26.14        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-A2LB TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       16.18        12.82        17.56        28.70        36.43        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MH 
        8.98         1.94        23.01        12.56        13.97        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.87        18.58        13.08        12.92        18.48         5.19 
TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       13.58        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       16.14        17.62        15.62         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
       13.58         8.15        17.72        21.30         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       10.55       163.30        66.05        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        50.70        38.24        52.01        15.02        13.58 
TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      165.73        18.81        15.35        56.15        11.18        20.32 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF 
       29.72        22.16         2.24        16.70        25.58         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN 
       26.96        26.24        24.66         0.92         1.22        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-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         7.56        27.35        14.96 
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-A5C1 TCGA-FD-A62N 
        5.36         5.69         8.25        27.45        58.92         2.70 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TK 
       13.35        62.86        18.81         6.15        12.69        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
       31.07        12.66         8.94        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       20.12        66.02         6.94        70.32        21.40        19.13 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
       15.91        14.07        17.75        24.92         8.94         7.73 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 
        3.12         2.20        11.31        18.97        32.78        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI 
        5.62         4.73        32.98        19.10        19.82        36.49 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC 
        8.58         1.51        64.01        12.16         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41N 
       27.68        11.70        17.72         1.81        16.27        52.73 
TCGA-KQ-A41Q TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
       46.98        15.32        15.58        21.07        13.48        16.67 
TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA 
       16.54        22.68        76.01        78.25       112.83         3.91 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SH 
        6.21         3.85        45.04        97.45       125.49        64.80 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
        3.22        15.98        66.41        34.45        14.93         4.21 
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-AAME TCGA-XF-AAMG 
        2.24        16.27        66.64         2.10        92.98       110.60 
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-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 
       18.15         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        25.41        21.11        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN 
       28.41         3.48        64.08        58.72        88.87        20.22 
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 
       12.23 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.62 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           166.03            165.73 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            17.42             17.16 
[1] "0.1 - 166.0 (17.4)" "0.6 - 165.7 (17.2)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         0       44        40       57
  3P GAIN WILD-TYPE       2       85       100       78
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               44                85
  STAGE III              40               100
  STAGE IV               57                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         39  62  26
  3P GAIN WILD-TYPE       84 133  32
D5V4, multiclass
          clus
vv         3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1+T2              39                84
  T3                    62               133
  T4                    26                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
  3P GAIN MUTATED    67  19  34   4
  3P GAIN WILD-TYPE 168  28  41   5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              67               168
  N1              19                28
  N2              34                41
  N3               4                 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    62   6
  3P GAIN WILD-TYPE 130   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     62    6
  3P GAIN WILD-TYPE  130    5
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              62               130
  1               6                 5
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    32 110
  3P GAIN WILD-TYPE  75 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     32  110
  3P GAIN WILD-TYPE   75  191
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              32                75
  MALE               110               191
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED   123   7
  3P GAIN WILD-TYPE 241  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    123    7
  3P GAIN WILD-TYPE  241   12
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO              123               241
  YES               7                12
[1] 2 2
[1] FALSE
D5V9, continuous
D5V10, continuous
D5V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED      10                         5   122
  3P GAIN WILD-TYPE    33                        17   205
D5V12, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                  10                33
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                 122               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"
D5V13, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3 128
  3P GAIN WILD-TYPE   6 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3  128
  3P GAIN WILD-TYPE    6  241
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             128               241
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    96  81
  3Q GAIN WILD-TYPE 133  96
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              177               229 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               81                96 
$`3Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA84 
       24.13        16.27        16.77        34.98        27.62        15.12 
TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       47.80        17.42         7.33         6.74        12.39        13.15 
TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       19.04         5.06         8.35         8.25        17.16        20.48 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS 
        4.67         9.96        28.70        36.43        12.79        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
       12.59        12.13         4.90        15.12        18.48        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        1.84        21.86        66.41        18.41       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IS 
       46.68        17.95        87.32         4.80         8.22        50.27 
TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L 
       23.21        17.98        64.18        15.68        36.66        38.24 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 
      165.73       166.03        19.00        13.64        13.64        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 
       20.32        43.59        15.35         0.10        22.16        25.58 
TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q 
        0.56         4.24        24.03        13.68        12.95         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43P 
       32.02        33.04        22.52        24.30        23.41        27.35 
TCGA-FD-A43U TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE 
       20.91        18.08         7.10         6.28         6.15        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        2.27         3.06         4.31         9.67        10.65        17.23 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       11.08        61.94        48.00        59.31        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A3WC 
       17.62        29.36        20.71        15.81        14.07        17.75 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B 
        0.49         8.94        13.91         2.10        20.98         7.36 
TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       10.92         7.63        10.65         7.00        14.27        21.34 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
       20.28         8.48        27.35        19.07        22.72        19.40 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RH 
       38.60         9.01        25.02         3.45        21.24         9.07 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S 
       15.42        11.80        50.56        35.97        44.38         1.15 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       12.23        14.24         1.84        12.43        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD 
       37.05        86.83        69.34         3.02        29.56        17.82 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
       51.32        45.04         6.58        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SZ 
       17.88        79.66         3.22         5.98        12.76        28.24 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX 
       66.64        13.74         7.63        71.57         2.96         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 
       98.99        44.32        86.30        13.64        22.36        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RM TCGA-ZF-A9RN 
       30.28        94.29        13.41         3.48        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89        19.69        59.38        63.02        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       57.90        19.40        54.21 

$`3Q GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       11.97        94.88       104.65       108.95         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        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J 
       66.54        10.22        29.65         2.50        40.08         2.66 
TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.58        26.14        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F 
       14.89        14.96        16.18        12.82        17.56        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A3MI 
        8.98         1.94        23.01        13.97        13.08        12.16 
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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A5 
       18.58        13.08        12.92         5.19        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       19.00        16.70        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV 
      142.78        13.58         8.15        17.72        21.30         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81        10.55       163.30        66.05        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       67.36        50.70        52.01        15.02        13.58        18.81 
TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4XJ 
       15.35        56.15        11.18        38.83        29.72         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU 
       16.70         0.66        26.96        26.24        24.66         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         7.56 
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        12.66         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        70.32        21.40        19.13 
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 
       18.97        32.78        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        36.49         8.58         1.51        64.01 
TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ 
       12.16         2.76         9.14        27.68        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        16.27        52.73        46.98        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        16.54        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HD 
       78.25       112.83         3.91         6.21         3.85        97.45 
TCGA-XF-A8HE TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
      125.49        48.62        64.80        15.98        66.41        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        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        18.15         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        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       35.84        21.86        28.41        64.08        58.72        88.87 
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 
       12.23 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.62 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           166.03            163.30 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            17.88             16.54 
[1] "0.1 - 166.0 (17.9)" "0.6 - 163.3 (16.5)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         0       55        51       71
  3Q GAIN WILD-TYPE       2       74        89       64
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               55                74
  STAGE III              51                89
  STAGE IV               71                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         49  82  29
  3Q GAIN WILD-TYPE       74 113  29
D6V4, multiclass
          clus
vv         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1+T2              49                74
  T3                    82               113
  T4                    29                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
  3Q GAIN MUTATED    84  24  43   4
  3Q GAIN WILD-TYPE 151  23  32   5
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              84               151
  N1              24                23
  N2              43                32
  N3               4                 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    80   7
  3Q GAIN WILD-TYPE 112   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     80    7
  3Q GAIN WILD-TYPE  112    4
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              80               112
  1               7                 4
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    46 132
  3Q GAIN WILD-TYPE  61 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     46  132
  3Q GAIN WILD-TYPE   61  169
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              46                61
  MALE               132               169
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   158   8
  3Q GAIN WILD-TYPE 206  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    158    8
  3Q GAIN WILD-TYPE  206   11
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO              158               206
  YES               8                11
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, continuous
D6V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED      13                         9   151
  3Q GAIN WILD-TYPE    30                        13   176
D6V12, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                  13                30
  BLACK OR AFRICAN AMERICAN               9                13
  WHITE                                 151               176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     4 161
  3Q GAIN WILD-TYPE   5 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4  161
  3Q GAIN WILD-TYPE    5  208
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             161               208
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    29   9
  4P GAIN WILD-TYPE 200 168
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               38               368 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               168 
$`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        18.48         2.14        66.41       130.88         7.79 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-AA75 TCGA-E5-A4U1 TCGA-E7-A541 
       66.05        64.18        67.36        11.18        38.83        25.58 
TCGA-E7-A6MD TCGA-E7-A7DU TCGA-FD-A3NA TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TC 
        4.24         0.92        60.66         5.36        27.45         6.15 
TCGA-FD-A6TE TCGA-GD-A76B TCGA-GU-A42P TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A6FZ 
       12.36         7.36        10.92        22.72         9.01         1.81 
TCGA-KQ-A41R TCGA-MV-A51V TCGA-UY-A78N TCGA-UY-A78O TCGA-XF-A9T3 TCGA-YF-AA3L 
       44.38        13.48        86.83        76.01         2.24        11.97 
TCGA-ZF-A9R2 TCGA-ZF-AA5H 
       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 
       24.13        11.97        94.88       104.65       108.95         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        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       15.12        10.22        29.65         2.50        17.42        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        26.14        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-CF-A1HR TCGA-CF-A1HS 
       28.70        36.43        28.41         8.98        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        18.58        13.08        12.92         4.90        15.12 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 
        5.19        29.79         1.84        13.58        21.86        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       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 
       46.68        17.95       142.78        87.32         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        8.15         8.22        17.72        50.27        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       163.30        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       76.60        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       15.02        13.58       165.73       166.03        18.81        19.00 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       13.64        15.35        13.64        56.15        12.03        20.32 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       16.70         0.56         0.66        26.96        26.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       24.66         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-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-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85         7.56        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-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        8.25        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG 
       13.35        62.86        18.81        12.69         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        12.66        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        11.08        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        59.31        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        70.32        29.36        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       20.71        15.81        19.13        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-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         2.20        11.31        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       32.78        20.05         5.62         4.73        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-H4-A2HO 
        8.48        36.49        27.35         8.58        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40        38.60        64.01        12.16        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-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
       17.72        15.42        16.27        11.80        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       35.97        46.98         1.15        15.32        15.58        21.07 
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        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
        3.02       112.83         3.91        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        3.85        51.32        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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       79.66         3.22        15.98        66.41        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        4.21         5.98        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-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-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        18.15         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
        0.66        13.64        22.36        25.41        31.20        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       35.84        21.86        28.41        94.29        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       64.08        58.72        88.87        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 
       56.35        35.41        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  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 
           13.050            17.325 
[1] "0.9 - 130.9 (13.1)" "0.1 - 166.0 (17.3)"
[1] "hr=" "1.9"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         0       17        11       10
  4P GAIN WILD-TYPE       2      112       129      125
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               17               112
  STAGE III              11               129
  STAGE IV               10               125
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         19  16   3
  4P GAIN WILD-TYPE      104 179  55
D7V4, multiclass
          clus
vv         4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1+T2              19               104
  T3                    16               179
  T4                     3                55
[1] 3 2
[1] TRUE
[1] "dimension of 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    28   6   3   1
  4P GAIN WILD-TYPE 207  41  72   8
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              28               207
  N1               6                41
  N2               3                72
  N3               1                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    24   0
  4P GAIN WILD-TYPE 168  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     24    0
  4P GAIN WILD-TYPE  168   11
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              24               168
  1               0                11
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    14  24
  4P GAIN WILD-TYPE  93 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     14   24
  4P GAIN WILD-TYPE   93  277
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              14                93
  MALE                24               277
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    33   1
  4P GAIN WILD-TYPE 331  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     33    1
  4P GAIN WILD-TYPE  331   18
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               33               331
  YES               1                18
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, continuous
D7V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       5                         1    27
  4P GAIN WILD-TYPE    38                        21   300
D7V12, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   5                38
  BLACK OR AFRICAN AMERICAN               1                21
  WHITE                                  27               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"
D7V13, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  31
  4P GAIN WILD-TYPE   8 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   31
  4P GAIN WILD-TYPE    8  338
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              31               338
[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 210 170
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               26               380 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               170 
$`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 
       18.48         2.14        66.05        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        18.15        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 
       24.13        11.97        94.88       104.65       108.95         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        50.04 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       47.80        29.65         2.50        17.42        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 
       26.14        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-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
       36.43        28.41         8.98         1.94        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.10        11.34        18.58        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       15.12         5.19        29.79         1.84        13.58        21.86 
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        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      142.78        87.32         4.80        13.58         8.15         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-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       163.30        17.98        64.18        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       15.68        50.70        36.66        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       13.58       165.73       166.03        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 
       15.35        13.64        56.15        11.18        12.03        20.32 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        25.58         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
        4.24        24.03        24.66         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-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         7.56        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-A5BZ TCGA-FD-A5C1 
       11.01        19.33         5.69         8.25        27.45        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-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-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07        12.66        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        11.08        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       59.31        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        70.32        29.36        21.40        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       19.13        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-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        2.20        11.31        18.97         7.63        32.78        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        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       27.35         8.58        19.07         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       64.01        12.16        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-A6FZ 
        9.14        27.68         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
       15.42        16.27        11.80        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       46.98        44.38         1.15        15.32        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        16.54 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        38.99        17.62        37.05        22.68        86.83 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       78.25        69.34         3.02       112.83         3.91        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC 
       17.82         6.21         3.85        51.32        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-A9SK TCGA-XF-A9SL 
       48.62        64.80        79.66         3.22        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       34.45        14.93         4.21         5.98        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-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        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-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        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       31.20        30.28        35.84        21.86        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        64.08        58.72        88.87        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
        2.89        34.06        19.69         8.61        59.38        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       56.35        35.41        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  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 
           18.315            16.995 
[1] "2.1 - 76.0 (18.3)"  "0.1 - 166.0 (17.0)"
[1] "hr=" "1.7"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         0       13         7        6
  4Q GAIN WILD-TYPE       2      116       133      129
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               13               116
  STAGE III               7               133
  STAGE IV                6               129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  4Q GAIN MUTATED         13  13   0
  4Q GAIN WILD-TYPE      110 182  58
D8V4, multiclass
          clus
vv         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1+T2              13               110
  T3                    13               182
  T4                     0                58
[1] 3 2
[1] TRUE
[1] "dimension of 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 216  44  72   9
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              19               216
  N1               3                44
  N2               3                72
  N3               0                 9
[1] 4 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 176  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     16    0
  4Q GAIN WILD-TYPE  176   11
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              16               176
  1               0                11
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     8  18
  4Q GAIN WILD-TYPE  99 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      8   18
  4Q GAIN WILD-TYPE   99  283
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               8                99
  MALE                18               283
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    24   1
  4Q GAIN WILD-TYPE 340  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     24    1
  4Q GAIN WILD-TYPE  340   18
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               24               340
  YES               1                18
[1] 2 2
[1] FALSE
D8V9, continuous
D8V10, continuous
D8V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       3                         0    19
  4Q GAIN WILD-TYPE    40                        22   308
D8V12, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   3                40
  BLACK OR AFRICAN AMERICAN               0                22
  WHITE                                  19               308
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  21
  4Q GAIN WILD-TYPE   8 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   21
  4Q GAIN WILD-TYPE    8  348
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              21               348
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    92  74
  5P GAIN WILD-TYPE 137 103
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              166               240 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               74               103 
$`5P GAIN MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 
      108.95        27.62        50.04         0.62        41.75        10.22 
TCGA-5N-A9KI TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V 
        2.50         6.74        12.39        26.14        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A1HS 
        8.35        17.16        12.82         9.96        28.70        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A5UA TCGA-CU-A0YN 
       12.59        12.13        13.08        10.95        12.00        12.92 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IN 
       15.12         5.19        21.86       142.78        87.32         8.22 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B5 
       23.21         9.67        10.55        64.18        67.36        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       36.66        38.24        52.01        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        19.00        13.64        15.35        13.64        56.15 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6MD 
       15.35        38.83        29.72        22.16        25.58         4.24 
TCGA-E7-A7DV TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.22        12.95         8.09        32.02        16.77         8.94 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43Y 
       22.52        60.66         5.52        25.74        19.79        15.58 
TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N 
       26.73        19.33         5.36         8.25        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        7.10         6.28        13.35        18.81         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        3.06         4.31        10.85        17.23         3.25        11.08 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02        70.32        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP 
       20.71        15.81        24.92         0.49        13.91         2.10 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATO 
       20.98         7.36        10.92         7.63         5.62        10.65 
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        36.49 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RH 
        8.58        19.07        19.40        12.16         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       11.70         1.81        50.56        46.98        44.38         1.15 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78K 
       15.32        13.48        16.67         1.84        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HF 
       37.05        86.83        69.34        29.56         6.21        97.12 
TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9T3 
       48.62         3.22        15.98        34.45        14.93         2.24 
TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAN7 
       66.64        92.98        54.90         7.63         2.96        18.15 
TCGA-YF-AA3M TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RF 
       13.64        31.20        30.28        21.86        94.29        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       58.72        88.87        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       19.69        59.38        63.02        56.35        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       19.40         8.52        54.21        19.17 

$`5P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97        94.88       104.65         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-5N-A9KM TCGA-BL-A0C8 
       66.54        15.12        47.80        29.65        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         2.66         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB 
       17.88        19.50         5.06        14.96         8.25        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       20.48         4.67        17.56        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MI TCGA-CF-A47T 
        1.94        23.01        12.79        13.97        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO 
       11.34        11.34        11.87        18.58        13.08         4.90 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
       18.48        29.79         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-A3IK 
       17.62        15.62        46.68        17.95         7.79         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WW 
       13.58         8.15        17.72        50.27        21.30        20.81 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
      163.30        66.05        17.98        53.29        76.60        15.68 
TCGA-DK-AA6T TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3Y1 
       18.81        11.18        12.03        20.32        43.59         0.10 
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        26.96        26.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
       24.03        24.66         0.92        13.68        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SJ 
       14.37        33.04         4.01        12.62        27.98        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
       23.41        17.98        29.16        46.78        12.85         7.56 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35        14.96        20.91         3.62        53.88        11.01 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TF 
        5.69        27.45        18.08        62.86        12.69         2.27 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EF 
        9.67        31.07        12.66        10.65         8.94        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3C 
       48.00        15.95        26.93        33.01        17.62         6.94 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 
       21.40        19.13        15.91        14.07        17.75         8.94 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 
        7.73         3.12         2.20        11.31        18.97        32.78 
TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QK 
       20.05         4.73        32.98        21.34        19.82        27.35 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS 
       22.72         1.51        38.60        64.01         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB 
        3.45        21.24         2.76        27.68        17.72        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41P TCGA-LT-A5Z6 TCGA-LT-A8JT 
       16.27        11.80        52.73        35.97        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        16.54        12.43        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       78.25         3.02       112.83         3.91        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       51.32        45.04         6.58        97.45       125.49        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9ST 
        1.87        17.88        64.80        79.66        66.41         4.21 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        5.98        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       26.27        18.90        16.27         2.10        13.74        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
      110.60        11.31        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-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-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
       11.97        22.36        25.41        21.11        35.84        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA5N TCGA-ZF-AA5P 
       13.41         3.48         8.61        60.16         5.52        12.23 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.49              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           166.03            163.30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           16.965            17.490 
[1] "0.5 - 166.0 (17.0)" "0.1 - 163.3 (17.5)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         0       58        56       52
  5P GAIN WILD-TYPE       2       71        84       83
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               58                71
  STAGE III              56                84
  STAGE IV               52                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
  5P GAIN MUTATED         50  74  24
  5P GAIN WILD-TYPE       73 121  34
D9V4, multiclass
          clus
vv         5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1+T2              50                73
  T3                    74               121
  T4                    24                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
  5P GAIN MUTATED    89  23  26   3
  5P GAIN WILD-TYPE 146  24  49   6
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              89               146
  N1              23                24
  N2              26                49
  N3               3                 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"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    72   1
  5P GAIN WILD-TYPE 120  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     72    1
  5P GAIN WILD-TYPE  120   10
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              72               120
  1               1                10
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    42 124
  5P GAIN WILD-TYPE  65 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     42  124
  5P GAIN WILD-TYPE   65  177
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              42                65
  MALE               124               177
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   148   8
  5P GAIN WILD-TYPE 216  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    148    8
  5P GAIN WILD-TYPE  216   11
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              148               216
  YES               8                11
[1] 2 2
[1] FALSE
D9V9, continuous
D9V10, continuous
D9V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED      11                        10   139
  5P GAIN WILD-TYPE    32                        12   188
D9V12, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                  11                32
  BLACK OR AFRICAN AMERICAN              10                12
  WHITE                                 139               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3 154
  5P GAIN WILD-TYPE   6 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  154
  5P GAIN WILD-TYPE    6  215
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             154               215
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    30  23
  5Q GAIN WILD-TYPE 199 154
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               53               353 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               23               154 
$`5Q GAIN MUTATED`
TCGA-5N-A9KI TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A42C TCGA-CF-A1HS 
        2.50         6.74        26.14        14.89        28.70        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A6AV TCGA-DK-A6B6 
       12.59        12.13       142.78        87.32        64.18        36.66 
TCGA-DK-AA6L TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E7-A541 TCGA-E7-A85H TCGA-FD-A5BU 
       38.24        13.64        56.15        25.58        12.95        19.33 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FT-A3EE TCGA-G2-A2EO 
       58.92         6.28        12.36         4.31         3.25        59.31 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GD-A76B TCGA-GU-A762 
       29.36        20.71        15.81        24.92         7.36         7.63 
TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-K4-A4AC TCGA-K4-A5RH 
       14.27         8.48        36.49         8.58         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX 
       11.70         1.81         1.15        15.32        13.48         1.84 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9T5 TCGA-XF-AAMJ 
       37.05        86.83         6.21        48.62        66.64        54.90 
TCGA-XF-AAMZ TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       44.32        57.90        19.40         8.52        54.21 

$`5Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 
       15.12        10.22        47.80        29.65        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66        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-A20V 
       12.16        17.88        19.50         5.06        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        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A3MI 
        1.94        23.01        12.79        13.97        13.08        12.16 
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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       18.58        13.08        12.92         4.90        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        29.79         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        46.68        17.95         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        4.80        13.58         8.15         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       163.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       66.05        17.98        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        52.01        15.02        13.58       165.73       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA75 TCGA-DK-AA76 
       18.81        19.00        13.64        15.35        11.18        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       20.32        43.59        15.35        38.83        29.72         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.24         4.24        24.03        24.66         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        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-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         7.56 
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-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       18.08         2.70         7.10        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
        6.15        12.69         2.27         3.06         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P 
       31.07        12.66        10.65        17.23         8.94        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM 
       20.12        17.62        66.02         6.94        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 
       19.13        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-A763 TCGA-GU-A764 TCGA-GU-A766 
       10.92        11.31        18.97        32.78        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
        4.73        10.65        32.98         7.00        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       19.82        20.28        27.35        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60        64.01         9.01        12.16        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB 
        3.45        21.24         2.76        27.68        17.72        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       16.27        11.80        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       44.38        15.58        21.07        12.23        16.67        14.24 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O 
       16.54        12.43        38.99        17.62        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       78.25        69.34         3.02       112.83         3.91        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       17.82         3.85        51.32        45.04         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-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       79.66         3.22        15.98        66.41        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        4.21         5.98        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-AAML 
       13.74        92.98        10.82       110.60        11.31         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-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 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        22.36        25.41        21.11        31.20        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       35.84        21.86        28.41        94.29        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       64.08        58.72        88.87        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-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       56.35        35.41        19.17         5.52        12.23 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.15              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           142.78            166.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            15.32             17.42 
[1] "1.1 - 142.8 (15.3)" "0.1 - 166.0 (17.4)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         0       15        21       17
  5Q GAIN WILD-TYPE       2      114       119      118
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               15               114
  STAGE III              21               119
  STAGE IV               17               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
  5Q GAIN MUTATED         14  27   7
  5Q GAIN WILD-TYPE      109 168  51
D10V4, multiclass
          clus
vv         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1+T2              14               109
  T3                    27               168
  T4                     7                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
  5Q GAIN MUTATED    29   9   8   0
  5Q GAIN WILD-TYPE 206  38  67   9
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              29               206
  N1               9                38
  N2               8                67
  N3               0                 9
[1] 4 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 173  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     19    0
  5Q GAIN WILD-TYPE  173   11
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              19               173
  1               0                11
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    14  39
  5Q GAIN WILD-TYPE  93 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     14   39
  5Q GAIN WILD-TYPE   93  262
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              14                93
  MALE                39               262
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    48   3
  5Q GAIN WILD-TYPE 316  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     48    3
  5Q GAIN WILD-TYPE  316   16
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               48               316
  YES               3                16
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, continuous
D10V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       6                         1    44
  5Q GAIN WILD-TYPE    37                        21   283
D10V12, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   6                37
  BLACK OR AFRICAN AMERICAN               1                21
  WHITE                                  44               283
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  50
  5Q GAIN WILD-TYPE   8 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   50
  5Q GAIN WILD-TYPE    8  319
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              50               319
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    44  34
  6P GAIN WILD-TYPE 185 143
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               78               328 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               34               143 
$`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         8.15        10.55 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E7-A541 TCGA-E7-A6ME 
       67.36        15.68        56.15        11.18        25.58        24.03 
TCGA-FD-A3B7 TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A5BU TCGA-FD-A5C1 TCGA-FD-A6TC 
        4.01        19.79        12.85        19.33        58.92         6.15 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-AA3B 
        2.27         3.06        10.65         3.25        11.08        66.02 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A4ZW 
       21.40        20.71        15.81        15.91        24.92         0.49 
TCGA-GD-A2C5 TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-AATO TCGA-GU-AATP 
        7.73        10.92        18.97         7.63        10.65        32.98 
TCGA-GV-A6ZA TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-AAQO TCGA-LC-A66R 
       22.72        12.16         9.14         9.07        11.80        15.32 
TCGA-LT-A5Z6 TCGA-SY-A9G0 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       15.58        12.43        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
       69.34         3.02        29.56         6.21         3.85        51.32 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9T5 TCGA-XF-AAMG 
        6.58        97.45        14.93         4.21        66.64       110.60 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-ZF-A9R4 TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4R 
        7.63        71.57        30.28        58.72        20.22        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       19.69        59.38        63.02        19.40        54.21        19.17 

$`6P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04 
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        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        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        26.14        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        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        1.94        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       18.58        13.08        12.92         4.90        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        29.79         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        46.68        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        4.80        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       163.30        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       64.18        53.29        76.60        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T 
       52.01        15.02        13.58       165.73       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 
       19.00        13.64        15.35        13.64        12.03        20.32 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        29.72         0.10        22.16 
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        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
        4.24        24.66         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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        8.94        33.04        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-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       46.78         7.56        27.35        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX 
       15.58        26.73        53.88        11.01         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        8.25        27.45        18.08         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
       13.35        62.86        18.81        12.69        12.36         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        12.66        17.23         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        48.00        15.95        26.93        59.31        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        70.32        29.36 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP 
       19.13        14.07        17.75         8.94        13.91         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 
        3.12        20.98         2.20         7.36        11.31        32.78 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05         5.62         4.73         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        36.49        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        64.01 
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-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N 
       11.70        17.72         1.81        15.42        16.27        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A8JT 
       50.56        35.97        46.98        44.38         1.15        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        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD 
       38.99        17.62        78.25       112.83         3.91        17.82 
TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       45.04       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL 
       48.62        64.80        79.66         3.22        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       34.45         5.98        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-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR 
       13.74        92.98        10.82        11.31        54.90        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        18.15 
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 
       22.36        25.41        21.11        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL 
       28.41        94.29        13.41         3.48        64.08        88.87 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
       47.84         2.89         8.61        60.16        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90         8.52         5.52        12.23 

  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 
           16.520            17.325 
[1] "0.5 - 130.9 (16.5)" "0.1 - 166.0 (17.3)"
[1] "hr=" "1"  
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         0       22        26       30
  6P GAIN WILD-TYPE       2      107       114      105
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               22               107
  STAGE III              26               114
  STAGE IV               30               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
  6P GAIN MUTATED         26  36  13
  6P GAIN WILD-TYPE       97 159  45
D11V4, multiclass
          clus
vv         6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1+T2              26                97
  T3                    36               159
  T4                    13                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
  6P GAIN MUTATED    41  11  17   2
  6P GAIN WILD-TYPE 194  36  58   7
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              41               194
  N1              11                36
  N2              17                58
  N3               2                 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"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    30   2
  6P GAIN WILD-TYPE 162   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     30    2
  6P GAIN WILD-TYPE  162    9
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              30               162
  1               2                 9
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    16  62
  6P GAIN WILD-TYPE  91 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     16   62
  6P GAIN WILD-TYPE   91  239
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              16                91
  MALE                62               239
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    65   5
  6P GAIN WILD-TYPE 299  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     65    5
  6P GAIN WILD-TYPE  299   14
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               65               299
  YES               5                14
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, continuous
D11V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       6                         2    69
  6P GAIN WILD-TYPE    37                        20   258
D11V12, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   6                37
  BLACK OR AFRICAN AMERICAN               2                20
  WHITE                                  69               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"
D11V13, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2  70
  6P GAIN WILD-TYPE   7 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2   70
  6P GAIN WILD-TYPE    7  299
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              70               299
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    25  16
  6Q GAIN WILD-TYPE 204 161
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               41               365 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16               161 
$`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         8.15        10.55        67.36 
TCGA-DK-AA75 TCGA-E7-A6ME TCGA-FD-A3SS TCGA-FD-A5C1 TCGA-FJ-A3ZE TCGA-GC-A3BM 
       11.18        24.03        12.85        58.92        10.65        21.40 
TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GU-A42P TCGA-GU-AATO TCGA-K4-A4AC 
       15.81        24.92         0.49        10.92        10.65         9.14 
TCGA-K4-A5RH TCGA-K4-AAQO TCGA-LC-A66R TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A9PH 
        9.07        11.80        15.32        37.05        86.83        51.32 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-ZF-A9R4 
        6.58        97.45        66.64       110.60        71.57        30.28 
TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X 
       58.72        20.22        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 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       47.80        29.65         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66         6.74        12.39        13.15        19.04        26.14 
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-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25        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        36.43        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        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.87        18.58        13.08        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       18.48         5.19        29.79         1.84        13.58        21.86 
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-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      142.78         4.80        13.58         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       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
       17.98        64.18        53.29        76.60        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       36.66        38.24        52.01        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        18.81        19.00        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       56.15        12.03        20.32        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       29.72         0.10        22.16         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24         4.24        24.66 
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-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79         7.56        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-A5BV 
       15.58        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O 
        5.69         8.25        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-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        12.66        17.23         8.94         3.25        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        48.00        15.95        26.93        59.31        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        70.32 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       29.36        20.71        19.13        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-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        2.20         7.36        11.31        18.97         7.63        32.78 
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        36.49 
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        64.01         9.01        12.16        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       21.24         2.76        27.68        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       15.42        16.27        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        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        16.54        12.43        38.99 
TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       17.62        22.68        76.01        78.25        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
      112.83         3.91        29.56        17.82         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       45.04       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL 
       48.62        64.80        79.66         3.22        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       34.45        14.93         4.21         5.98        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-AAMX 
       54.90         7.63        91.73         2.96         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        18.15         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        22.36        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       31.20        35.84        21.86        28.41        94.29        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R 
        3.48        64.08        88.87        47.84         2.89        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
        8.61        60.16        56.35        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21        19.17         5.52        12.23 

  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 
            17.16             17.23 
[1] "0.5 - 130.9 (17.2)" "0.1 - 166.0 (17.2)"
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         0       13        16       12
  6Q GAIN WILD-TYPE       2      116       124      123
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               13               116
  STAGE III              16               124
  STAGE IV               12               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
  6Q GAIN MUTATED         15  18   6
  6Q GAIN WILD-TYPE      108 177  52
D12V4, multiclass
          clus
vv         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1+T2              15               108
  T3                    18               177
  T4                     6                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
  6Q GAIN MUTATED    24   6   4   2
  6Q GAIN WILD-TYPE 211  41  71   7
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              24               211
  N1               6                41
  N2               4                71
  N3               2                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    21   1
  6Q GAIN WILD-TYPE 171  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     21    1
  6Q GAIN WILD-TYPE  171   10
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              21               171
  1               1                10
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     6  35
  6Q GAIN WILD-TYPE 101 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6   35
  6Q GAIN WILD-TYPE  101  266
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               6               101
  MALE                35               266
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    32   5
  6Q GAIN WILD-TYPE 332  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     32    5
  6Q GAIN WILD-TYPE  332   14
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               32               332
  YES               5                14
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, continuous
D12V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       5                         0    36
  6Q GAIN WILD-TYPE    38                        22   291
D12V12, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   5                38
  BLACK OR AFRICAN AMERICAN               0                22
  WHITE                                  36               291
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1  37
  6Q GAIN WILD-TYPE   8 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   37
  6Q GAIN WILD-TYPE    8  332
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              37               332
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    94  77
  7P GAIN WILD-TYPE 135 100
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              171               235 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               77               100 
$`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        29.65        12.39         6.58 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       26.14        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        36.43        28.41        23.01        12.79 
TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A5U8 TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
       12.13        12.16        13.12        12.92         4.90        18.48 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       13.58        21.86       130.88        17.95         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
       87.32         4.80        13.58         8.15         8.22        50.27 
TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 
       23.21        66.05        17.98        64.18        67.36        36.66 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA75 
       38.24        15.02       165.73       166.03        19.00        11.18 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DU 
       43.59        15.35        22.16        25.58        24.03         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 
        1.22        13.68         8.09        32.02         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         7.56        27.35        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
        3.62        26.73         5.36        27.45        18.08        58.92 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
        7.10         6.28         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        3.06         9.67        31.07        10.65        17.23         3.25 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F 
       11.08        59.31        17.62        66.02        70.32        29.36 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 
       21.40        20.71        15.91        14.07        13.91         7.73 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A766 TCGA-GU-AATP 
       20.98         2.20        10.92        11.31         5.62        32.98 
TCGA-GU-AATQ TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ 
        7.00        19.82        27.35         8.58        22.72        19.40 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ 
       38.60         9.01        12.16         9.07        11.70         1.81 
TCGA-K4-A83P TCGA-KQ-A41P TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX 
       16.27        35.97         1.15        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        38.99        22.68        86.83        76.01        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HD 
        3.02         3.91        29.56         6.21        51.32        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       97.12        15.35        48.62        79.66         3.22        15.98 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T5 
       14.93         4.21         5.98        21.04         2.24        66.64 
TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 
      110.60        71.57         2.96         6.77        98.99        56.48 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9RD 
       75.39        18.15        13.64        22.36        31.20        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4V 
       64.08        58.72        20.22         2.89        34.06        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5H 
       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 
       24.13        11.97        94.88       104.65       108.95         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        50.04        51.16        66.54 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       13.15        19.04        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
       14.96         5.06         8.35         4.67         9.96        17.56 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH 
        8.98         1.94        12.56        13.97        12.59        13.08 
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-A9FL 
       12.00        12.10        11.34        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 
       13.08        15.12         5.19        29.79         1.84         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-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV 
       17.62        15.62        46.68        17.72        21.30         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
       20.81        10.55       163.30        53.29        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X 
       50.70        52.01        13.58        18.81        13.64        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        56.15        12.03        20.32        38.83        29.72 
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        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       26.24         4.24        24.66        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       14.37        16.77        33.04        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-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       19.79        14.96        15.58        53.88        11.01        19.33 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        5.69         8.25         2.70        13.35        62.86        18.81 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ 
        4.31        10.85        12.66         8.94        61.94        48.00 
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-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.81        19.13        17.75        24.92         0.49         8.94 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        2.10         3.12         7.36        18.97         7.63        32.78 
TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       20.05         4.73        10.65        14.27        21.34        19.10 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OF 
       20.28         8.48        36.49        19.07         1.51        64.01 
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-A6MB TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q 
       17.72        15.42        11.80        52.73        50.56        46.98 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       44.38        15.58        21.07        12.23        16.67        14.24 
TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
       16.54        17.62        37.05        78.25       112.83        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
        3.85        45.04         6.58       125.49         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       64.80        66.41        34.45        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        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       21.11        30.28        35.84        21.86        28.41        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W 
        3.48        88.87        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 
       56.35        35.41        57.90        19.40        54.21         5.52 
TCGA-ZF-AA5P 
       12.23 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.62              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           166.03            163.30 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            17.16             17.42 
[1] "0.6 - 166.0 (17.2)" "0.1 - 163.3 (17.4)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         0       41        62       67
  7P GAIN WILD-TYPE       2       88        78       68
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               41                88
  STAGE III              62                78
  STAGE IV               67                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
  7P GAIN MUTATED         41  89  30
  7P GAIN WILD-TYPE       82 106  28
D13V4, multiclass
          clus
vv         7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1+T2              41                82
  T3                    89               106
  T4                    30                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
  7P GAIN MUTATED    88  24  34   8
  7P GAIN WILD-TYPE 147  23  41   1
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              88               147
  N1              24                23
  N2              34                41
  N3               8                 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    75   5
  7P GAIN WILD-TYPE 117   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     75    5
  7P GAIN WILD-TYPE  117    6
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              75               117
  1               5                 6
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    46 125
  7P GAIN WILD-TYPE  61 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     46  125
  7P GAIN WILD-TYPE   61  176
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              46                61
  MALE               125               176
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   158   4
  7P GAIN WILD-TYPE 206  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    158    4
  7P GAIN WILD-TYPE  206   15
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              158               206
  YES               4                15
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, continuous
D13V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED      11                        10   143
  7P GAIN WILD-TYPE    32                        12   184
D13V12, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                  11                32
  BLACK OR AFRICAN AMERICAN              10                12
  WHITE                                 143               184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     4 150
  7P GAIN WILD-TYPE   5 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4  150
  7P GAIN WILD-TYPE    5  219
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             150               219
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    82  67
  7Q GAIN WILD-TYPE 147 110
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              149               257 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               67               110 
$`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        29.65        12.39         6.58        26.14         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        36.43        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CF-A5U8 TCGA-CU-A0YN TCGA-CU-A0YO 
       23.01        12.79        12.13        13.12        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       18.48        13.58       112.44        46.68        17.95         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 
       87.32        13.58         8.22        50.27        23.21        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T 
       67.36        36.66        38.24       165.73       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       19.00        13.64        11.18        20.32        43.59        15.35 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q 
       22.16        25.58         0.92         1.22        13.68         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SQ TCGA-FD-A3SS 
       16.77         8.94         4.01        22.52        46.78        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV 
        7.56        27.35        20.91         3.62        26.73         5.36 
TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TD 
       27.45        58.92         7.10         6.28         6.15        12.69 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        2.27         4.31         9.67        10.65        17.23         3.25 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F 
       11.08        59.31        17.62        66.02        70.32        29.36 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 
       21.40        20.71        15.91        14.07        13.91         7.73 
TCGA-GD-A3OS TCGA-GU-A764 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       20.98        20.05        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND 
        8.58        19.07        22.72        19.40        38.60         9.01 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41P 
       21.24         9.07        11.70         1.81        16.27        35.97 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX TCGA-SY-A9G0 
       44.38         1.15        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 
       38.99        22.68        86.83        76.01         3.02        29.56 
TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        6.21        51.32         6.58        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9SU 
       15.35        48.62        79.66         3.22        14.93         5.98 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 
       66.64       110.60        71.57         6.77        98.99        56.48 
TCGA-XF-AAN5 TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG 
       75.39        22.36        31.20        28.41        13.41        58.72 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4X TCGA-ZF-AA5H 
       20.22         2.89        34.06        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 
       24.13        11.97        94.88       104.65       108.95         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        50.04        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.74        13.15        19.04        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-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 
        4.67         9.96        17.56        28.70         8.98         1.94 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       12.56        13.97        12.59        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA 
       12.66        12.46        12.10        12.62        12.26        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
       15.12         5.19        29.79         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       142.78         4.80         8.15        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       163.30        66.05 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M 
       64.18        53.29        76.60        15.68        50.70        52.01 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       15.02        13.58        15.35        13.64        56.15        12.03 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        29.72         0.10         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B6 
       14.07        12.95        15.32        14.37        32.02        33.04 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.62        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y 
       29.16         5.52        25.74        19.79        14.96        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       53.88        11.01        19.33         5.69         8.25        18.08 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE TCGA-FD-A6TG 
        2.70        13.35        62.86        18.81        12.36         3.06 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.85        31.07        12.66         8.94        61.94        48.00 
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-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.81        19.13        17.75        24.92         0.49         8.94 
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-A766 TCGA-GU-A767 TCGA-GU-AATO 
       18.97         7.63        32.78         5.62         4.73        10.65 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        1.51        64.01        12.16        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N 
        9.14        27.68        17.72        15.42        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       50.56        46.98        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-A8OB 
       14.24        16.54        17.62        37.05        78.25        69.34 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HH 
      112.83         3.91        17.82         3.85        45.04         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST 
       17.88        64.80        15.98        66.41        34.45         4.21 
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-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90         2.24        16.27         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT 
       10.82        11.31        54.90         7.63        91.73         2.96 
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-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       13.64        25.41        21.11        30.28        35.84        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4T 
       94.29         3.48        64.08        88.87        47.84        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        59.38        60.16        56.35        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        54.21         5.52        12.23 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.62              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           166.03            163.30 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            19.07             16.27 
[1] "0.6 - 166.0 (19.1)" "0.1 - 163.3 (16.3)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         0       40        50       59
  7Q GAIN WILD-TYPE       2       89        90       76
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               40                89
  STAGE III              50                90
  STAGE IV               59                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
  7Q GAIN MUTATED         41  70  29
  7Q GAIN WILD-TYPE       82 125  29
D14V4, multiclass
          clus
vv         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1+T2              41                82
  T3                    70               125
  T4                    29                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
  7Q GAIN MUTATED    77  19  31   9
  7Q GAIN WILD-TYPE 158  28  44   0
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              77               158
  N1              19                28
  N2              31                44
  N3               9                 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    62   5
  7Q GAIN WILD-TYPE 130   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     62    5
  7Q GAIN WILD-TYPE  130    6
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              62               130
  1               5                 6
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    42 108
  7Q GAIN WILD-TYPE  65 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     42  108
  7Q GAIN WILD-TYPE   65  193
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              42                65
  MALE               108               193
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   138   6
  7Q GAIN WILD-TYPE 226  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    138    6
  7Q GAIN WILD-TYPE  226   13
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              138               226
  YES               6                13
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, continuous
D14V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       9                        10   126
  7Q GAIN WILD-TYPE    34                        12   201
D14V12, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN              10                12
  WHITE                                 126               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"
D14V13, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     3 133
  7Q GAIN WILD-TYPE   6 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3  133
  7Q GAIN WILD-TYPE    6  236
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             133               236
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    53  37
  8P GAIN WILD-TYPE 176 140
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               90               316 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               37               140 
$`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 
       29.65         6.74        12.39        19.04        26.14         5.06 
TCGA-BT-A2LA TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MG 
       17.16        36.43         1.94        23.01        13.97        12.13 
TCGA-CF-A5UA TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A3IQ 
       12.00        13.58        66.41        16.14        17.95        17.72 
TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA6U 
       50.27        10.55        17.98        36.66       165.73        19.00 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A85H 
       13.64        56.15        43.59        22.16        24.03        12.95 
TCGA-E7-A97P TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BX 
       14.37        27.98        60.66        20.91        53.88         5.69 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-G2-A2ES TCGA-G2-A3VY 
       58.92         7.10         9.67        10.65        33.01        17.62 
TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI 
       66.02        21.40        20.71         7.00        14.27        36.49 
TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A83P TCGA-KQ-A41P 
       22.72        38.60        64.01        11.70        16.27        35.97 
TCGA-KQ-A41S TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 
        1.15        13.48        16.67         1.84        12.43        38.99 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HD 
       22.68        86.83         3.02         6.21         3.85        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SP TCGA-XF-A9SU 
       97.12        15.35        48.62        64.80        14.93         5.98 
TCGA-XF-A9SY TCGA-XF-A9T6 TCGA-XF-AAMY TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 
       21.04         2.10        98.99        18.15        13.64        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       31.20        20.22         2.89        63.02        56.35        35.41 

$`8P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
        0.62        66.54        10.22         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        7.33         2.66         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-A20X 
       19.50         5.06        14.89        14.96         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-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF 
       28.70        28.41         8.98        12.79        12.56        12.59 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.87        18.58        13.08        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
       18.48         5.19        29.79         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        46.68         7.79       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       13.58         8.15         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       163.30        66.05        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       67.36        15.68        50.70        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA75 
       13.58       166.03        18.81        13.64        15.35        11.18 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        20.32        15.35        38.83        29.72         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        25.58         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       26.24         4.24        24.66         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.07        15.32         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL 
       33.04         4.01        12.62        22.52        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-A43X TCGA-FD-A43Y 
       12.85         7.56        27.35        14.96         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       26.73        11.01        19.33         5.36         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       18.08         2.70         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-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        31.07        12.66        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       11.08        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO 
        7.23        20.12         6.94        70.32        29.36        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       19.13        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        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       32.78        20.05         5.62         4.73        10.65        32.98 
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-A5ND TCGA-HQ-A5NE 
        8.58        19.07         1.51        19.40         9.01        12.16 
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-KQ-A41N 
        9.07        17.72         1.81        15.42        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       50.56        46.98        44.38        15.32        15.58        21.07 
TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O 
       12.23        14.24        16.54        17.62        37.05        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       78.25        69.34       112.83         3.91        29.56        17.82 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       51.32        45.04         6.58       125.49         1.87        17.88 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST 
       79.66         3.22        15.98        66.41        34.45         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       12.76        11.90        23.64        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27        66.64        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
        2.96         8.32         6.77        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-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R4 
        9.63         0.66        11.97        22.36        25.41        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       35.84        21.86        28.41        94.29        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4T 
       64.08        58.72        88.87        47.84        34.06        19.69 
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-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21        19.17         5.52        12.23 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.15              0.10 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           165.73            166.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           19.630            16.405 
[1] "1.1 - 165.7 (19.6)" "0.1 - 166.0 (16.4)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         0       28        34       27
  8P GAIN WILD-TYPE       2      101       106      108
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               28               101
  STAGE III              34               106
  STAGE IV               27               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
  8P GAIN MUTATED         30  42  13
  8P GAIN WILD-TYPE       93 153  45
D15V4, multiclass
          clus
vv         8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1+T2              30                93
  T3                    42               153
  T4                    13                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
  8P GAIN MUTATED    50  13  12   2
  8P GAIN WILD-TYPE 185  34  63   7
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              50               185
  N1              13                34
  N2              12                63
  N3               2                 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    46   3
  8P GAIN WILD-TYPE 146   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     46    3
  8P GAIN WILD-TYPE  146    8
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              46               146
  1               3                 8
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    21  69
  8P GAIN WILD-TYPE  86 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     21   69
  8P GAIN WILD-TYPE   86  232
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              21                86
  MALE                69               232
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    82   4
  8P GAIN WILD-TYPE 282  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     82    4
  8P GAIN WILD-TYPE  282   15
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               82               282
  YES               4                15
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, continuous
D15V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED      10                         4    69
  8P GAIN WILD-TYPE    33                        18   258
D15V12, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                  10                33
  BLACK OR AFRICAN AMERICAN               4                18
  WHITE                                  69               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"
D15V13, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2  74
  8P GAIN WILD-TYPE   7 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   74
  8P GAIN WILD-TYPE    7  295
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              74               295
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   117  86
  8Q GAIN WILD-TYPE 112  91
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              203               203 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               86                91 
$`8Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA80 
       24.13        11.97       104.65        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        29.65 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A20W 
        6.74        12.39        19.04        26.14         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        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S 
        1.94        23.01        13.97        12.13        13.08        10.95 
TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A3KJ 
       12.62        12.00        11.34        11.87        12.92        18.48 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19         1.84        13.58        21.86        66.41        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 
      130.88       112.44        16.14        17.95       142.78        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X1 
        8.22        17.72        50.27        23.21        10.55        66.05 
TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R 
       17.98        15.68        36.66        52.01        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      166.03        19.00        13.64        13.64        56.15        11.18 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DU 
       43.59        38.83        22.16        25.58        24.03         0.92 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B6 TCGA-FD-A3N6 
       13.68        12.95        14.37         8.09        33.04        27.98 
TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS 
       60.66        46.78         7.56        20.91        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
       11.01         5.36         5.69        18.08        58.92         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI 
        6.28        13.35        12.69        12.36         4.31         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3VY 
       12.66        10.65         3.25        15.95        33.01        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3WC 
       66.02        70.32        21.40        20.71        19.13        17.75 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-AATP TCGA-GU-AATQ 
        2.10         3.12        20.98         7.36        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-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       36.49        22.72        38.60        64.01         9.01        12.16 
TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        2.76         9.07        11.70         1.81        15.42        16.27 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT 
       52.73        35.97        44.38         1.15        15.32        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       13.48        12.23        16.67        14.24         1.84        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OC 
       38.99        17.62        22.68        86.83        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
      112.83        29.56         6.21         3.85        51.32        45.04 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       97.45        97.12        15.35        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 
        3.22        14.93         5.98        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        18.15 
TCGA-YC-A89H TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       18.84        13.64        22.36        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N 
       30.28        28.41         3.48        58.72        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        56.35        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       19.40         8.52        54.21        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 
       94.88       108.95         8.35        16.83        16.77        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM 
       34.98        27.62        50.04        66.54         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
       40.08         7.33         2.66         6.58        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A2LD 
       17.88        19.50         5.06        14.89        14.96        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-CF-A1HR 
        4.67        12.82         9.96        17.56        28.70        12.79 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.56        12.59        12.16        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FL TCGA-CF-A9FM 
       12.26        13.12        12.10        11.34        18.58        13.08 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
        4.90        15.12        29.79         2.14        19.00        16.70 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62        15.62        46.68         7.79         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AV 
        8.15        21.30         9.67        20.81       163.30        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q 
       53.29        76.60        67.36        50.70        38.24        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A3X6 
       18.81        15.35        12.03        20.32        15.35        29.72 
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        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 
       26.24         4.24        24.66         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        11.08        61.94        48.00        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC 
        7.23        20.12         6.94        29.36        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        18.97         7.63        32.78 
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-KQ-A41O TCGA-KQ-A41Q 
        9.14        27.68        17.72        11.80        50.56        46.98 
TCGA-LT-A5Z6 TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A9PA 
       15.58        16.54        37.05        76.01        78.25         3.91 
TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SK 
       17.82         6.58       125.49         1.87        17.88        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
       66.41        34.45         4.21        11.90        23.64        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90        16.27        66.64        13.74        92.98        10.82 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
       71.57        91.73         6.77        44.32        56.48        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       86.30        27.06         3.88         9.63         0.66        11.97 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RL 
       35.84        21.86        94.29        13.41        64.08        88.87 
TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA5P 
       47.84        34.06        19.69        59.38        12.23 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.62              0.10 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           166.03            163.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            17.98             16.70 
[1] "0.6 - 166.0 (18.0)" "0.1 - 163.3 (16.7)"
[1] "hr=" "1.2"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         0       62        73       66
  8Q GAIN WILD-TYPE       2       67        67       69
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               62                67
  STAGE III              73                67
  STAGE IV               66                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
  8Q GAIN MUTATED         63 99 28
  8Q GAIN WILD-TYPE       60 96 30
D16V4, multiclass
          clus
vv         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1+T2              63                60
  T3                    99                96
  T4                    28                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
  8Q GAIN MUTATED   114  26  34   4
  8Q GAIN WILD-TYPE 121  21  41   5
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             114               121
  N1              26                21
  N2              34                41
  N3               4                 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   95  6
  8Q GAIN WILD-TYPE 97  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     95    6
  8Q GAIN WILD-TYPE   97    5
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              95                97
  1               6                 5
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    53 150
  8Q GAIN WILD-TYPE  54 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     53  150
  8Q GAIN WILD-TYPE   54  151
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              53                54
  MALE               150               151
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   180  12
  8Q GAIN WILD-TYPE 184   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    180   12
  8Q GAIN WILD-TYPE  184    7
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              180               184
  YES              12                 7
[1] 2 2
[1] FALSE
D16V9, continuous
D16V10, continuous
D16V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED      18                         8   164
  8Q GAIN WILD-TYPE    25                        14   163
D16V12, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                  18                25
  BLACK OR AFRICAN AMERICAN               8                14
  WHITE                                 164               163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     5 176
  8Q GAIN WILD-TYPE   4 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5  176
  8Q GAIN WILD-TYPE    4  193
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 4
  NOT HISPANIC OR LATINO             176               193
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    42  26
  9P GAIN WILD-TYPE 187 151
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               68               338 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               26               151 
$`9P GAIN MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-BL-A3JM TCGA-BT-A2LA TCGA-BT-A3PJ 
       24.13        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        15.12         5.19       130.88       112.44 
TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-FD-A3B3 
       17.95        87.32         8.15        36.66       165.73        32.02 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A5BT TCGA-FD-A62N 
       33.04        22.52        23.41        27.35        11.01         2.70 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-AA3D 
        2.27         4.31        10.65        61.94        48.00        70.32 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A763 TCGA-GV-A3JZ 
       20.71        15.91         7.73         2.10        32.78        19.82 
TCGA-GV-A3QI TCGA-GV-A40G TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-LC-A66R TCGA-SY-A9G0 
       36.49        19.07        12.16         1.81        15.32        12.43 
TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG 
       17.62        78.25        29.56         6.58        97.45        15.35 
TCGA-XF-A9SG TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAML 
       48.62        34.45        14.93        21.04         2.24         7.63 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 
       27.06        75.39        13.64        22.36        30.28        21.86 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V 
       64.08        58.72        47.84         2.89        19.69        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA58 
       63.02        54.21 

$`9P GAIN WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        94.88       104.65       108.95         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        50.04         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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       29.65         2.50        17.42        40.08         7.33         2.66 
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        26.14        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-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK 
        8.35         8.25        16.18        20.48         4.67         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
       17.56        28.70        36.43        28.41         8.98        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL 
       11.87        18.58        13.08         4.90        18.48        29.79 
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-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       19.00        16.70        16.14        17.62        15.62        46.68 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ 
        7.79       142.78         4.80        13.58         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-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      163.30        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       67.36        15.68        50.70        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        18.81        19.00        13.64        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       13.64        56.15        11.18        12.03        20.32        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        25.58         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
        4.24        24.03        24.66         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 
       14.07        12.95        15.32        14.37         8.09        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        8.94         4.01        12.62        27.98        60.66        24.30 
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         7.56        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-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-A6TG 
       62.86        18.81         6.15        12.69        12.36         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85        31.07        12.66        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        3.25        11.08        15.95        26.93        59.31        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        29.36 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       21.40        15.81        19.13        14.07        17.75        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        0.49         8.94        13.91         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        7.36        10.92        11.31        18.97         7.63        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-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
       21.34        19.10        20.28         8.48        27.35         8.58 
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        64.01         9.01 
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-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        9.07        11.70        17.72        15.42        16.27        11.80 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       52.73        50.56        35.97        46.98        44.38         1.15 
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-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
        1.84        16.54        38.99        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD 
       76.01        69.34         3.02       112.83         3.91        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF 
        6.21         3.85        51.32        45.04       125.49        97.12 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.87        17.88        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       66.41         4.21         5.98        12.76        11.90        23.64 
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-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-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-AAN7 
       44.32        56.48        30.94        61.45        86.30        18.15 
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        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       21.11        31.20        35.84        28.41        94.29        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4W 
        3.48        88.87        20.22        34.06         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       56.35        35.41        57.90        19.40         8.52        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.81              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           165.73            166.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           20.265            16.605 
[1] "1.8 - 165.7 (20.3)" "0.1 - 166.0 (16.6)"
[1] "hr=" "1.4"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         0       20        25       23
  9P GAIN WILD-TYPE       2      109       115      112
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               20               109
  STAGE III              25               115
  STAGE IV               23               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
  9P GAIN MUTATED         18  34   9
  9P GAIN WILD-TYPE      105 161  49
D17V4, multiclass
          clus
vv         9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1+T2              18               105
  T3                    34               161
  T4                     9                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    36   5  15   3
  9P GAIN WILD-TYPE 199  42  60   6
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              36               199
  N1               5                42
  N2              15                60
  N3               3                 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"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    30   3
  9P GAIN WILD-TYPE 162   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     30    3
  9P GAIN WILD-TYPE  162    8
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              30               162
  1               3                 8
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15  53
  9P GAIN WILD-TYPE  92 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15   53
  9P GAIN WILD-TYPE   92  248
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              15                92
  MALE                53               248
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    58   2
  9P GAIN WILD-TYPE 306  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     58    2
  9P GAIN WILD-TYPE  306   17
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               58               306
  YES               2                17
[1] 2 2
[1] FALSE
D17V9, continuous
D17V10, continuous
D17V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       2                         3    59
  9P GAIN WILD-TYPE    41                        19   268
D17V12, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   2                41
  BLACK OR AFRICAN AMERICAN               3                19
  WHITE                                  59               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"
D17V13, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  60
  9P GAIN WILD-TYPE   7 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   60
  9P GAIN WILD-TYPE    7  309
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              60               309
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    34  22
  9Q GAIN WILD-TYPE 195 155
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               56               350 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               22               155 
$`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        17.95         8.15         8.22        36.66 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3SL TCGA-FD-A5BT 
       52.01       165.73        32.02        16.77        23.41        11.01 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZE 
        5.36         2.70        12.69         4.31        10.85        10.65 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC 
       61.94        48.00        70.32        20.71        15.91        17.75 
TCGA-GC-A3YS TCGA-GD-A76B TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-LC-A66R 
       24.92         7.36        19.40        12.16         1.81        15.32 
TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HC 
       17.62        78.25        69.34        29.56         6.21         6.58 
TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9T3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       97.45        15.35        48.62         2.24        27.06        75.39 
TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4T 
       30.28        21.86        58.72        47.84         2.89        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA58 
       59.38        54.21 

$`9Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04         0.62        41.75        66.54        10.22        47.80 
TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       29.65         2.50        17.42        40.08         7.33         2.66 
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        26.14        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-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35         8.25        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        36.43        28.41         8.98 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       18.48         5.19        29.79         1.84        13.58        21.86 
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-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        46.68         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32         4.80        13.58        17.72        50.27        21.30 
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       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       50.70        38.24        15.02        13.58       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       19.00        13.64        15.35        13.64        56.15        11.18 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        20.32        43.59        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
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-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.37         8.09         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-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         7.56 
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-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       53.88        19.33         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       58.92         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
        6.15        12.36         2.27         3.06         9.67        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK 
       12.66        17.23         8.94         3.25        11.08        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        59.31        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
       66.02         6.94        29.36        21.40        15.81        19.13 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07         0.49         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20        10.92        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        32.78        20.05         5.62         4.73        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        36.49        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS 
       22.72         1.51        38.60        64.01         9.01        25.02 
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-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       11.70        17.72        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 
       50.56        35.97        46.98        44.38         1.15        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-A78L TCGA-UY-A78M TCGA-UY-A78N 
       16.54        12.43        38.99        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       76.01         3.02       112.83         3.91        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI 
       51.32        45.04       125.49        97.12         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
       64.80        79.66         3.22        15.98        66.41        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       14.93         4.21         5.98        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-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-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       86.30        18.15         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        22.36        25.41        21.11        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       35.84        28.41        94.29        13.41         3.48        64.08 
TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X 
       88.87        20.22        34.06         8.61        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       56.35        35.41        57.90        19.40         8.52        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.81              0.10 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           165.73            166.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           17.850            16.735 
[1] "1.8 - 165.7 (17.9)" "0.1 - 166.0 (16.7)"
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         0       14        24       18
  9Q GAIN WILD-TYPE       2      115       116      117
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               14               115
  STAGE III              24               116
  STAGE IV               18               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
  9Q GAIN MUTATED         11  30   7
  9Q GAIN WILD-TYPE      112 165  51
D18V4, multiclass
          clus
vv         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1+T2              11               112
  T3                    30               165
  T4                     7                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
  9Q GAIN MUTATED    35   4  11   1
  9Q GAIN WILD-TYPE 200  43  64   8
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              35               200
  N1               4                43
  N2              11                64
  N3               1                 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"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    21   4
  9Q GAIN WILD-TYPE 171   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     21    4
  9Q GAIN WILD-TYPE  171    7
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              21               171
  1               4                 7
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    17  39
  9Q GAIN WILD-TYPE  90 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     17   39
  9Q GAIN WILD-TYPE   90  262
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              17                90
  MALE                39               262
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    49   1
  9Q GAIN WILD-TYPE 315  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     49    1
  9Q GAIN WILD-TYPE  315   18
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               49               315
  YES               1                18
[1] 2 2
[1] FALSE
D18V9, continuous
D18V10, continuous
D18V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       2                         4    47
  9Q GAIN WILD-TYPE    41                        18   280
D18V12, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   2                41
  BLACK OR AFRICAN AMERICAN               4                18
  WHITE                                  47               280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  48
  9Q GAIN WILD-TYPE   7 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   48
  9Q GAIN WILD-TYPE    7  321
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              48               321
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    57  59
  10P GAIN WILD-TYPE 172 118
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               116                290 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                59                118 
$`10P GAIN MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA81 
       24.13        16.27        16.77        17.16         0.62        41.75 
TCGA-4Z-AA84 TCGA-5N-A9KI TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V 
       15.12         2.50         6.58        26.14         5.06         5.06 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A42E TCGA-CF-A1HS TCGA-CF-A3MF 
        8.35        16.18        12.82        36.43        12.56        12.59 
TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A5UA TCGA-CU-A0YN TCGA-DK-A1A3 TCGA-DK-A1A5 
       12.13        12.16        12.00        12.92        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3X1 
       66.41       112.44        87.32        13.58         8.22        66.05 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-E5-A4U1 TCGA-E7-A6MD 
       15.68        36.66        15.02       166.03        38.83         4.24 
TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       13.68        14.37         8.09        33.04        60.66        24.30 
TCGA-FD-A3SS TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       12.85        26.73        53.88        27.45        18.08        58.92 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FT-A3EE TCGA-FT-A61P 
       12.36         2.27         3.06         9.67         3.25        11.08 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A4ZW 
       33.01        20.12        66.02        29.36        19.13         0.49 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A767 TCGA-GU-AATO 
        7.73        20.98         2.20        10.92         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       32.98         7.00        21.34        19.82        20.28         8.48 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        8.58        22.72        38.60        64.01         9.01        12.16 
TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41P 
       25.02         9.14        27.68        17.72         1.81        35.97 
TCGA-KQ-A41S TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
        1.15        38.99        17.62        37.05        22.68        86.83 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SH 
       69.34         3.91        51.32        97.12        15.35        64.80 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMH 
        3.22        15.98        14.93        23.64       110.60        11.31 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
        7.63         2.96        13.64        22.36        31.20        30.28 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-AA4R TCGA-ZF-AA51 TCGA-ZF-AA52 
       28.41        94.29        64.08        34.06        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 
       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        94.88       104.65       108.95         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        50.04        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80        29.65        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74        12.39        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA 
       17.88        19.50        14.89        14.96         8.25        17.16 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
       20.48         4.67         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-A3MH 
        8.98         1.94        23.01        12.79        13.97        13.08 
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-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL 
       13.12        12.10        11.34        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08         4.90        15.12        18.48         5.19        29.79 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        1.84        13.58        18.41        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
      142.78         4.80         8.15        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       23.21         9.67        20.81        10.55       163.30        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L 
       64.18        53.29        76.60        67.36        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       52.01        13.58       165.73        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 
       15.35        13.64        56.15        11.18        12.03        20.32 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        15.35        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        25.58         0.56         0.66        26.96        26.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H 
       24.03        24.66         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         7.56        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        12.66        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 
       48.00        15.95        26.93        59.31         7.23        17.62 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
        6.94        70.32        21.40        20.71        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        18.97         7.63        32.78 
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        36.49        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-KQ-A41N 
        9.07        11.70        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       50.56        46.98        44.38        15.32        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        16.54 
TCGA-SY-A9G0 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB 
       12.43        76.01        78.25         3.02       112.83        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       17.82         6.21         3.85        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SL 
      125.49         1.87        17.88        48.62        79.66        66.41 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45         4.21         5.98        12.76        11.90        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-AAMJ TCGA-XF-AAMQ 
        2.10        13.74        92.98        10.82        54.90        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-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.15 
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        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG 
       21.11        35.84        21.86        13.41         3.48        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       88.87        47.84        20.22         2.89        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       59.38        60.16        63.02         8.52        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.49               0.10 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            166.03             165.73 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            17.670             16.995 
[1] "0.5 - 166.0 (17.7)" "0.1 - 165.7 (17.0)"
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         0       34        37       44
  10P GAIN WILD-TYPE       2       95       103       91
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                34                 95
  STAGE III               37                103
  STAGE IV                44                 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
  10P GAIN MUTATED         34  59  15
  10P GAIN WILD-TYPE       89 136  43
D19V4, multiclass
          clus
vv         10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1+T2               34                 89
  T3                     59                136
  T4                     15                 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
  10P GAIN MUTATED    51  17  23   5
  10P GAIN WILD-TYPE 184  30  52   4
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               51                184
  N1               17                 30
  N2               23                 52
  N3                5                  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    51   3
  10P GAIN WILD-TYPE 141   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     51    3
  10P GAIN WILD-TYPE  141    8
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               51                141
  1                3                  8
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    25  91
  10P GAIN WILD-TYPE  82 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     25   91
  10P GAIN WILD-TYPE   82  210
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               25                 82
  MALE                 91                210
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   102   4
  10P GAIN WILD-TYPE 262  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    102    4
  10P GAIN WILD-TYPE  262   15
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO               102                262
  YES                4                 15
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, continuous
D19V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       9                         2    98
  10P GAIN WILD-TYPE    34                        20   229
D19V12, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    9                 34
  BLACK OR AFRICAN AMERICAN                2                 20
  WHITE                                   98                229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3  99
  10P GAIN WILD-TYPE   6 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3   99
  10P GAIN WILD-TYPE    6  270
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               99                270
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    17  28
  10Q GAIN WILD-TYPE 212 149
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                45                361 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                28                149 
$`10Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-5N-A9KI TCGA-BT-A0S7 
       24.13         0.62        41.75        15.12         2.50         6.58 
TCGA-BT-A20R TCGA-BT-A20V TCGA-CF-A3MF TCGA-CF-A3MI TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.06         5.06        12.59        12.16        21.86        66.41 
TCGA-DK-A1AD TCGA-DK-A3IN TCGA-DK-A6B2 TCGA-E5-A4U1 TCGA-E7-A6MD TCGA-E7-A7PW 
      112.44         8.22        15.68        38.83         4.24        13.68 
TCGA-E7-A97Q TCGA-FD-A3B6 TCGA-FD-A3SS TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FD-A6TI 
        8.09        33.04        12.85        26.73        27.45         9.67 
TCGA-G2-AA3B TCGA-GC-A3RB TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-HQ-A2OE 
       66.02        19.13         4.73        10.65         7.00        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A9PH 
       64.01         9.01        38.99        22.68        86.83        51.32 
TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMT 
       15.35        15.98        23.64       110.60        11.31         2.96 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R9 
       22.36        31.20        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        94.88       104.65       108.95         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 
       50.04        51.16        66.54        10.22        47.80        29.65 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       17.42        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        26.14        12.16        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.89        14.96         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         8.98         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       12.56        13.97        12.13        13.08        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-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90        15.12        18.48         5.19        29.79 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        1.84        13.58         2.14        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88        16.14        17.62        15.62        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       142.78        87.32         4.80        13.58         8.15 
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       163.30        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       76.60        67.36        50.70        36.66        38.24        52.01 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       15.02        13.58       165.73       166.03        18.81        19.00 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 
       13.64        15.35        13.64        56.15        11.18        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       20.32        43.59        15.35        29.72         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        25.58         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN 
       26.24        24.03        24.66         0.92         1.22        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-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-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79         7.56        27.35        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       15.58        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        8.25        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-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.27         3.06         4.31        10.85        31.07        12.66 
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        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       48.00        15.95        26.93        59.31        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        70.32        29.36        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       20.71        15.81        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-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3JV 
        7.63        32.78        20.05         5.62        32.98        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        36.49 
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-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       12.16        25.02         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        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       16.27        11.80        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       44.38         1.15        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        16.54        12.43 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       17.62        37.05        76.01        78.25        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
      112.83         3.91        29.56        17.82         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
       45.04         6.58        97.45       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-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       34.45        14.93         4.21         5.98        12.76        11.90 
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-AAMJ 
       66.64         2.10        13.74        92.98        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
        7.63        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        18.15         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       11.97        13.64        25.41        21.11        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        94.29        13.41         3.48        64.08        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       88.87        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        56.35        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        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  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 
             15.98              17.23 
[1] "0.6 - 112.4 (16.0)" "0.1 - 166.0 (17.2)"
[1] "hr=" "1.5"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         0        9        12       23
  10Q GAIN WILD-TYPE       2      120       128      112
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                 9                120
  STAGE III               12                128
  STAGE IV                23                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
  10Q GAIN MUTATED         13  21  11
  10Q GAIN WILD-TYPE      110 174  47
D20V4, multiclass
          clus
vv         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1+T2               13                110
  T3                     21                174
  T4                     11                 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
  10Q GAIN MUTATED    17  11  11   2
  10Q GAIN WILD-TYPE 218  36  64   7
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               17                218
  N1               11                 36
  N2               11                 64
  N3                2                  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"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    22   1
  10Q GAIN WILD-TYPE 170  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     22    1
  10Q GAIN WILD-TYPE  170   10
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               22                170
  1                1                 10
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    11  34
  10Q GAIN WILD-TYPE  96 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     11   34
  10Q GAIN WILD-TYPE   96  267
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               11                 96
  MALE                 34                267
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    41   1
  10Q GAIN WILD-TYPE 323  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     41    1
  10Q GAIN WILD-TYPE  323   18
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                41                323
  YES                1                 18
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, continuous
D20V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       4                         1    36
  10Q GAIN WILD-TYPE    39                        21   291
D20V12, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                1                 21
  WHITE                                   36                291
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  36
  10Q GAIN WILD-TYPE   8 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   36
  10Q GAIN WILD-TYPE    8  333
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               36                333
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    14  14
  11P GAIN WILD-TYPE 215 163
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                28                378 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                14                163 
$`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        20.71 
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        36.49         8.58 
TCGA-K4-A4AC TCGA-KQ-A41P TCGA-LC-A66R TCGA-PQ-A6FI TCGA-UY-A9PB TCGA-UY-A9PF 
        9.14        35.97        15.32        12.23        29.56         3.85 
TCGA-XF-A8HF TCGA-XF-A9SY TCGA-XF-AAMH TCGA-YF-AA3M 
       97.12        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 
       24.13        11.97        94.88       104.65       108.95         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        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       15.12        10.22        47.80        29.65         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         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        26.14        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-A3PK TCGA-BT-A42B 
       17.16        16.18        20.48         4.67         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        36.43        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.87        18.58        13.08        15.12        18.48         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       29.79         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        46.68        17.95         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         4.80        13.58         8.15         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       50.27        21.30        23.21        20.81       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q 
       50.70        36.66        38.24        52.01        15.02        13.58 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
      165.73       166.03        18.81        19.00        13.64        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       13.64        56.15        11.18        12.03        20.32        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70        25.58         0.56        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       24.03        24.66         0.92        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-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         7.56        27.35        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-A62N 
        5.69         8.25        27.45        18.08        58.92         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-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.36         2.27         3.06         4.31        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       12.66        10.65        17.23         8.94         3.25        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        48.00        15.95        26.93        59.31        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        70.32 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
       29.36        21.40        15.81        19.13        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-A767 TCGA-GU-AATO TCGA-GU-AATP 
       18.97        32.78        20.05         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-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 
       64.01         9.01        12.16        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        2.76        27.68         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q 
       15.42        16.27        11.80        52.73        50.56        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
       44.38         1.15        15.58        21.07        13.48        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84        16.54        12.43        38.99        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        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PH 
        3.02       112.83         3.91        17.82         6.21        51.32 
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-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       17.88        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       66.41        34.45        14.93         4.21         5.98        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-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-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-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        18.15         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        22.36        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        31.20        30.28        35.84        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       94.29        13.41         3.48        64.08        58.72        88.87 
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        56.35        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        54.21        19.17         5.52        12.23 

  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 
             11.77              17.67 
[1] "0.7 - 97.1 (11.8)"  "0.1 - 166.0 (17.7)"
[1] "hr=" "1.7"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         0       10         8       10
  11P GAIN WILD-TYPE       2      119       132      125
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                10                119
  STAGE III                8                132
  STAGE IV                10                125
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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  13   5
  11P GAIN WILD-TYPE      115 182  53
D21V4, multiclass
          clus
vv         11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1+T2                8                115
  T3                     13                182
  T4                      5                 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
  11P GAIN MUTATED    14   2   5   4
  11P GAIN WILD-TYPE 221  45  70   5
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               14                221
  N1                2                 45
  N2                5                 70
  N3                4                  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   1
  11P GAIN WILD-TYPE 184  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    1
  11P GAIN WILD-TYPE  184   10
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                8                184
  1                1                 10
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  26
  11P GAIN WILD-TYPE 105 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   26
  11P GAIN WILD-TYPE  105  275
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                105
  MALE                 26                275
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    26   1
  11P GAIN WILD-TYPE 338  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     26    1
  11P GAIN WILD-TYPE  338   18
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                26                338
  YES                1                 18
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, continuous
D21V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       1                         0    26
  11P GAIN WILD-TYPE    42                        22   301
D21V12, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                 42
  BLACK OR AFRICAN AMERICAN                0                 22
  WHITE                                   26                301
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  27
  11P GAIN WILD-TYPE   8 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   27
  11P GAIN WILD-TYPE    8  342
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               27                342
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    23  25
  11Q GAIN WILD-TYPE 206 152
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                48                358 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                25                152 
$`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         8.15        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        70.32        29.36 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JZ 
       20.71        15.91         7.63         5.62         4.73        19.82 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-K4-A4AC TCGA-KQ-A41P TCGA-LC-A66R TCGA-PQ-A6FI 
       20.28         8.58         9.14        35.97        15.32        12.23 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PF TCGA-XF-A8HF 
        1.84        12.43        22.68         3.02         3.85        97.12 
TCGA-XF-A9SY TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMX TCGA-YF-AA3M TCGA-ZF-AA51 
       21.04        11.31         7.63         6.77        13.64        56.35 

$`11Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       47.80        29.65         2.50        17.42        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 
       26.14        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        36.43 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         8.98         1.94        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       15.12        18.48         5.19        29.79         1.84        13.58 
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        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN 
        7.79       142.78        87.32         4.80        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-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      163.30        66.05        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       15.68        50.70        36.66        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       13.58       165.73       166.03        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC 
       15.35        13.64        56.15        11.18        20.32        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70        25.58         0.56        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       24.03        24.66         0.92        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-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-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       12.85         7.56        14.96        20.91         3.62        15.58 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       53.88        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
       18.08        58.92         2.70         7.10        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-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        12.66        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 
       11.08        61.94        48.00        15.95        26.93        59.31 
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-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       21.40        15.81        19.13        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-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        18.97 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
       32.78        20.05        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
       21.34        19.10         8.48        36.49        27.35        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        64.01         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
       12.16        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        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       11.80        52.73        50.56        46.98        44.38         1.15 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
       15.58        21.07        13.48        16.67        14.24        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       38.99        17.62        37.05        86.83        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       69.34       112.83         3.91        29.56        17.82         6.21 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       51.32        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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU 
       15.98        66.41        34.45        14.93         4.21         5.98 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       12.76        11.90        23.64        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-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       10.82       110.60        54.90        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32        98.99        44.32        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        18.15         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        22.36        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       31.20        30.28        35.84        21.86        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        64.08        58.72        88.87        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-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        63.02        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21        19.17         5.52        12.23 

  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 
            12.625             17.670 
[1] "0.6 - 97.1 (12.6)"  "0.1 - 166.0 (17.7)"
[1] "hr=" "1.7"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         0       16         9       23
  11Q GAIN WILD-TYPE       2      113       131      112
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                16                113
  STAGE III                9                131
  STAGE IV                23                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
  11Q GAIN MUTATED         15  22   9
  11Q GAIN WILD-TYPE      108 173  49
D22V4, multiclass
          clus
vv         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1+T2               15                108
  T3                     22                173
  T4                      9                 49
[1] 3 2
[1] TRUE
[1] "dimension of 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   4
  11Q GAIN WILD-TYPE 214  42  60   5
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               21                214
  N1                5                 42
  N2               15                 60
  N3                4                  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   2
  11Q GAIN WILD-TYPE 175   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     17    2
  11Q GAIN WILD-TYPE  175    9
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               17                175
  1                2                  9
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     7  41
  11Q GAIN WILD-TYPE 100 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7   41
  11Q GAIN WILD-TYPE  100  260
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                7                100
  MALE                 41                260
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    42   1
  11Q GAIN WILD-TYPE 322  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     42    1
  11Q GAIN WILD-TYPE  322   18
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                42                322
  YES                1                 18
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, continuous
D22V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       2                         2    42
  11Q GAIN WILD-TYPE    41                        20   285
D22V12, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    2                 41
  BLACK OR AFRICAN AMERICAN                2                 20
  WHITE                                   42                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"
D22V13, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  44
  11Q GAIN WILD-TYPE   8 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   44
  11Q GAIN WILD-TYPE    8  325
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               44                325
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    62  53
  12P GAIN WILD-TYPE 167 124
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               115                291 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                53                124 
$`12P GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 
       24.13        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        26.14        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        36.43 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YN 
       12.13        13.08        12.00        11.34        11.34        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A3IM TCGA-DK-A3IS 
        4.90        15.12        21.86        66.41         8.15        50.27 
TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       10.55        66.05        64.18        67.36        15.68        36.66 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA75 
       15.02       166.03        18.81        19.00        15.35        11.18 
TCGA-DK-AA76 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 
       12.03        22.16         0.56        24.03        32.02        33.04 
TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BX 
       60.66        12.85        27.35        53.88         5.36         5.69 
TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FJ-A3Z7 TCGA-FT-A61P 
       27.45         6.28        13.35        18.81        31.07        11.08 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       59.31        17.62        66.02        21.40        20.71        15.81 
TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GU-A762 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JZ 
       14.07        13.91         7.63        10.65         7.00        19.82 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A2OE 
        8.48        36.49        27.35         8.58        19.07        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
       64.01         9.01        12.16         3.45        21.24         9.14 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41P TCGA-MV-A51V TCGA-SY-A9G5 
       11.70         1.81        16.27        35.97        13.48        38.99 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PE TCGA-XF-A9SI 
       76.01        78.25        69.34         3.91         6.21        79.66 
TCGA-XF-A9SK TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMY 
       15.98         5.98        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        18.15        13.64        25.41 
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 
       94.88       104.65       108.95         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        50.04 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        47.80        29.65         2.50        17.42 
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-A20O TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA 
       12.16        19.50        14.89        14.96         8.35        17.16 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        4.67        17.56        28.70        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MI 
       23.01        12.79        12.56        13.97        12.59        12.16 
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-A7I0 TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A3KJ 
       13.12        12.10        11.87        18.58        13.08        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 
        5.19        29.79         1.84        13.58         2.14        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        46.68        17.95         7.79       142.78        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        4.80        13.58         8.22        17.72        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        20.81       163.30        17.98        53.29        76.60 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6W 
       50.70        38.24        52.01        13.58       165.73        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        56.15        20.32        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF 
       29.72         0.10         2.24        16.70        25.58         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.96        26.24         4.24        24.66         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-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-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-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       46.78        19.79         7.56        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C0 
       15.58        26.73        11.01        19.33         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         2.70         7.10        62.86         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-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
       12.66        10.65        17.23         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        33.01         7.23        20.12 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
        6.94        70.32        29.36        19.13        15.91        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         0.49         8.94         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        18.97 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JV 
       32.78        20.05         5.62         4.73        32.98        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10        20.28        22.72         1.51        19.40 
TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB 
       25.02         2.76        27.68         9.07        17.72        15.42 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       11.80        52.73        50.56        46.98        44.38         1.15 
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-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84        16.54        12.43        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
       86.83         3.02       112.83        29.56        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       51.32        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-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX 
       66.41        34.45        14.93         4.21        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-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       11.31        54.90        71.57        91.73         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        30.94        61.45        27.06         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        9.63         0.66        11.97        22.36        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        28.41        94.29         3.48        64.08        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       88.87        47.84        20.22        34.06        19.69         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        63.02        56.35        35.41         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        12.23 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.56               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            166.03             165.73 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             16.18              17.42 
[1] "0.6 - 166.0 (16.2)" "0.1 - 165.7 (17.4)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         0       43        34       37
  12P GAIN WILD-TYPE       2       86       106       98
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                43                 86
  STAGE III               34                106
  STAGE IV                37                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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  56  12
  12P GAIN WILD-TYPE       86 139  46
D23V4, multiclass
          clus
vv         12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1+T2               37                 86
  T3                     56                139
  T4                     12                 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
  12P GAIN MUTATED    65  16  19   4
  12P GAIN WILD-TYPE 170  31  56   5
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               65                170
  N1               16                 31
  N2               19                 56
  N3                4                  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    56   3
  12P GAIN WILD-TYPE 136   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     56    3
  12P GAIN WILD-TYPE  136    8
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               56                136
  1                3                  8
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    32  83
  12P GAIN WILD-TYPE  75 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     32   83
  12P GAIN WILD-TYPE   75  218
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               32                 75
  MALE                 83                218
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   107   5
  12P GAIN WILD-TYPE 257  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    107    5
  12P GAIN WILD-TYPE  257   14
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO               107                257
  YES                5                 14
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, continuous
D23V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED      11                         5    93
  12P GAIN WILD-TYPE    32                        17   234
D23V12, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                   11                 32
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                   93                234
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     3 102
  12P GAIN WILD-TYPE   6 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3  102
  12P GAIN WILD-TYPE    6  267
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              102                267
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    54  38
  12Q GAIN WILD-TYPE 175 139
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                92                314 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                38                139 
$`12Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-BL-A3JM TCGA-BT-A20J 
       24.13        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-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A5UA TCGA-CF-A8HX 
       36.43        12.59        12.13        13.08        12.00        11.34 
TCGA-CF-A8HY TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
       11.34         4.90        15.12         1.84        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6AV 
       66.41       130.88        50.27        10.55        66.05        64.18 
TCGA-DK-A6B1 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       67.36        15.02       166.03        18.81        19.00        15.35 
TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3NA TCGA-FD-A43P 
       13.64        12.03         0.56        24.03        60.66        27.35 
TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A62S 
       15.58         5.36         5.69        27.45         6.28        13.35 
TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM 
       31.07        61.94        59.31        17.62        66.02        21.40 
TCGA-GC-A3I6 TCGA-GC-A6I3 TCGA-GU-AATO TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       20.71        13.91        10.65         8.48        36.49        27.35 
TCGA-GV-A40E TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A5RI TCGA-K4-A6FZ 
        8.58        38.60        64.01         3.45        11.70         1.81 
TCGA-K4-A83P TCGA-KQ-A41P TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A78P 
       16.27        35.97        13.48        38.99        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PE TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SU 
       69.34         3.91         6.21        79.66        15.98         5.98 
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 
       18.15        13.64        25.41        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 
       94.88       104.65       108.95         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        50.04 
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        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ 
        2.50        17.42        40.08         7.33         2.66        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T 
        6.58        13.15        26.14        12.16        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         8.35        17.16        20.48         4.67        12.82 
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-A1HS TCGA-CF-A27C TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.79        12.56        13.97        12.16        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-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.87        18.58        13.08        12.92        18.48         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
       29.79        13.58        18.41        19.00        16.70       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        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      142.78        87.32         4.80        13.58         8.15         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       17.72        21.30        23.21         9.67        20.81       163.30 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       17.98        53.29        76.60        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 
       38.24        52.01        13.58       165.73        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       11.18        20.32        43.59        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF 
        0.10        22.16         2.24        16.70        25.58         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.96        26.24         4.24        24.66         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         7.56 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
       19.33         8.25        18.08        58.92         2.70         7.10 
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        12.66        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK 
       17.23         8.94         3.25        11.08        48.00        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        70.32 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       29.36        15.81        19.13        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         0.49         8.94         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        18.97 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP 
        7.63        32.78        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-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07        22.72         1.51        19.40         9.01        12.16 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
       25.02        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q 
       17.72        15.42        11.80        52.73        50.56        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        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        16.54        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB 
       37.05        22.68        86.83         3.02       112.83        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       17.82         3.85        51.32        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
      125.49        97.12        15.35         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       64.80         3.22        66.41        34.45        14.93         4.21 
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-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 
        8.32         6.77        56.48        30.94        61.45        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       22.36        31.20        35.84        21.86        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        64.08        58.72        88.87        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X 
        2.89        34.06        19.69         8.61        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.56               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            166.03             165.73 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            16.225             17.325 
[1] "0.6 - 166.0 (16.2)" "0.1 - 165.7 (17.3)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         0       37        26       28
  12Q GAIN WILD-TYPE       2       92       114      107
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                37                 92
  STAGE III               26                114
  STAGE IV                28                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
  12Q GAIN MUTATED         32  40  11
  12Q GAIN WILD-TYPE       91 155  47
D24V4, multiclass
          clus
vv         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1+T2               32                 91
  T3                     40                155
  T4                     11                 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
  12Q GAIN MUTATED    55  12  16   1
  12Q GAIN WILD-TYPE 180  35  59   8
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               55                180
  N1               12                 35
  N2               16                 59
  N3                1                  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   3
  12Q GAIN WILD-TYPE 142   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     50    3
  12Q GAIN WILD-TYPE  142    8
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               50                142
  1                3                  8
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    27  65
  12Q GAIN WILD-TYPE  80 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     27   65
  12Q GAIN WILD-TYPE   80  236
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               27                 80
  MALE                 65                236
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    86   5
  12Q GAIN WILD-TYPE 278  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     86    5
  12Q GAIN WILD-TYPE  278   14
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                86                278
  YES                5                 14
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, continuous
D24V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED      11                         4    74
  12Q GAIN WILD-TYPE    32                        18   253
D24V12, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                   11                 32
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   74                253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  84
  12Q GAIN WILD-TYPE   7 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   84
  12Q GAIN WILD-TYPE    7  285
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               84                285
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    54  45
  13Q GAIN WILD-TYPE 175 132
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                99                307 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                45                132 
$`13Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-4Z-AA81 TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A0S7 
       24.13       108.95        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-A3MG TCGA-CF-A3MI TCGA-CF-A8HX TCGA-CU-A0YN TCGA-CU-A0YR 
       12.56        12.13        12.16        11.34        12.92        15.12 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A2HX TCGA-DK-A3IL TCGA-DK-A3IS TCGA-DK-A3IU 
        5.19        29.79        46.68        13.58        50.27        23.21 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6R 
       66.05        17.98        67.36        38.24        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-E5-A2PC TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DU 
      166.03        19.00        43.59        25.58        24.03         0.92 
TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B6 TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A43X 
       13.68         8.09        33.04        17.98        46.78         3.62 
TCGA-FD-A5BT TCGA-FD-A62O TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZE 
       11.01         7.10        12.36         3.06         4.31        10.65 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3OO 
       11.08        61.94        15.95        66.02        70.32        15.81 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ 
       17.75         0.49         2.10         4.73        10.65         7.00 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ 
       19.10        19.82        20.28         8.48        27.35        19.40 
TCGA-HQ-A5NE TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-AAQO TCGA-KQ-A41P TCGA-LC-A66R 
       12.16        27.68         9.07        11.80        35.97        15.32 
TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       13.48        14.24         1.84        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PH 
       22.68        76.01        78.25       112.83         3.91        51.32 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP 
       97.45        97.12        15.35         3.22        15.98        14.93 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-ZF-A9R0 
       71.57        91.73        98.99        56.48        61.45        22.36 
TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA56 
       19.69        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        94.88       104.65         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        50.04 
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        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ 
        2.50        17.42        40.08         7.33         2.66        12.39 
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20T 
       13.15        26.14        12.16        17.88         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
        5.06         8.35         8.25        17.16        16.18         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        9.96        17.56        28.70        36.43        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S 
       23.01        12.79        13.97        12.59        13.08        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-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.00        12.10        11.34        11.87        18.58        13.08 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        4.90        18.48         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        17.95         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
       87.32         4.80         8.15         8.22        17.72        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW 
        9.67        20.81        10.55       163.30        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6Q 
       76.60        15.68        50.70        36.66        52.01        13.58 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       18.81        13.64        15.35        13.64        56.15        11.18 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        20.32        15.35        38.83        29.72         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H 
       26.24         4.24        24.66         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-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       29.16         5.52        25.74        19.79        12.85         7.56 
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-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-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-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        6.15        12.69         2.27         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL 
       12.66        17.23         8.94         3.25        48.00        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       59.31        33.01         7.23        20.12        17.62         6.94 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       29.36        21.40        20.71        19.13        15.91        14.07 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       24.92         8.94        13.91         7.73         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        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW 
       32.78        20.05         5.62        32.98        14.27        21.34 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
       36.49         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 
       64.01         9.01        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.14        11.70        17.72         1.81        15.42        16.27 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 
       52.73        50.56        46.98        44.38         1.15        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78N 
       21.07        12.23        16.67        16.54        12.43        86.83 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34         3.02        29.56        17.82         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       45.04         6.58       125.49         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SU 
       64.80        79.66        66.41        34.45         4.21         5.98 
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-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 
        2.96         8.32         6.77        44.32        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        18.15         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        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        35.84        21.86        28.41        94.29        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        64.08        58.72        88.87        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
        2.89        34.06         8.61        59.38        60.16        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        57.90        19.40        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.49               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            166.03             163.30 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             17.98              16.77 
[1] "0.5 - 166.0 (18.0)" "0.1 - 163.3 (16.8)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         0       28        32       40
  13Q GAIN WILD-TYPE       2      101       108       95
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                28                101
  STAGE III               32                108
  STAGE IV                40                 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
  13Q GAIN MUTATED         27  49  15
  13Q GAIN WILD-TYPE       96 146  43
D25V4, multiclass
          clus
vv         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1+T2               27                 96
  T3                     49                146
  T4                     15                 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
  13Q GAIN MUTATED    54   9  25   6
  13Q GAIN WILD-TYPE 181  38  50   3
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               54                181
  N1                9                 38
  N2               25                 50
  N3                6                  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    46   5
  13Q GAIN WILD-TYPE 146   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     46    5
  13Q GAIN WILD-TYPE  146    6
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               46                146
  1                5                  6
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    22  78
  13Q GAIN WILD-TYPE  85 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     22   78
  13Q GAIN WILD-TYPE   85  223
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               22                 85
  MALE                 78                223
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    88   4
  13Q GAIN WILD-TYPE 276  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     88    4
  13Q GAIN WILD-TYPE  276   15
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                88                276
  YES                4                 15
[1] 2 2
[1] FALSE
D25V9, continuous
D25V10, continuous
D25V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       7                         3    88
  13Q GAIN WILD-TYPE    36                        19   239
D25V12, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    7                 36
  BLACK OR AFRICAN AMERICAN                3                 19
  WHITE                                   88                239
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  96
  13Q GAIN WILD-TYPE   9 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   96
  13Q GAIN WILD-TYPE    9  273
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               96                273
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    24  34
  14Q GAIN WILD-TYPE 205 143
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                58                348 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                34                143 
$`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        26.14         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         4.80         8.22        21.30        10.55 
TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA74 TCGA-E5-A2PC TCGA-FD-A3B3 TCGA-FD-A3B7 
       36.66       165.73        56.15        43.59        32.02         4.01 
TCGA-FD-A3N5 TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD 
       22.52        11.01        27.45         7.10        13.35        12.69 
TCGA-FD-A6TE TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GC-A3I6 
       12.36        10.65        26.93        59.31        21.40        20.71 
TCGA-GC-A3YS TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-AATO TCGA-GU-AATQ 
       24.92        20.98         2.20        10.92        10.65         7.00 
TCGA-GV-A3QH TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41O 
        8.48        21.24         9.14        11.70         1.81        50.56 
TCGA-LT-A5Z6 TCGA-PQ-A6FN TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A8HB TCGA-XF-A8HG 
       15.58        16.67        76.01       112.83        45.04        15.35 
TCGA-XF-A9SP TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-ZF-A9R0 
       14.93         2.24        10.82        71.57         2.96        22.36 
TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-AA4R TCGA-ZF-AA5H 
       13.41        58.72        34.06        19.17 

$`14Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       10.22        47.80        29.65         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         2.66         6.74        13.15        19.04        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        36.43        28.41 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        18.58        13.08         4.90        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        29.79         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        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS 
      142.78        87.32        13.58         8.15        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21         9.67        20.81       163.30        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        53.29        76.60        67.36        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       38.24        52.01        15.02        13.58       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 
       19.00        13.64        15.35        13.64        11.18        12.03 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       20.32        15.35        38.83        29.72         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        25.58         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.24         4.24        24.03        24.66         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-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       16.77         8.94        33.04        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         7.56        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-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         5.69         8.25        18.08        58.92         2.70 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG 
        6.28        62.86        18.81         6.15         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        4.31         9.67        10.85        31.07        12.66        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        11.08        61.94        48.00        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-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       70.32        29.36        15.81        19.13        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75         0.49         8.94        13.91         7.73         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        18.97         7.63        32.78 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05         5.62         4.73        32.98        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.10        19.82        20.28        36.49        27.35         8.58 
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        64.01 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R 
        9.01        12.16        25.02         3.45         2.76        27.68 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
        9.07        17.72        15.42        16.27        11.80        52.73 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT 
       35.97        46.98        44.38         1.15        15.32        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        12.23        14.24         1.84        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P 
       38.99        17.62        37.05        22.68        86.83        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       69.34         3.02         3.91        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.85        51.32         6.58        97.45       125.49        97.12 
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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       15.98        66.41        34.45         4.21         5.98        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-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG 
       16.27        66.64         2.10        13.74        92.98       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       11.31        54.90         7.63        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        18.15         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        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       30.28        35.84        21.86        28.41        94.29         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       64.08        88.87        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        56.35        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        54.21         5.52        12.23 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.81               0.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            165.73             166.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            15.465             17.590 
[1] "1.8 - 165.7 (15.5)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.5"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         0       14        25       19
  14Q GAIN WILD-TYPE       2      115       115      116
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                14                115
  STAGE III               25                115
  STAGE IV                19                116
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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  35   7
  14Q GAIN WILD-TYPE      113 160  51
D26V4, multiclass
          clus
vv         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1+T2               10                113
  T3                     35                160
  T4                      7                 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
  14Q GAIN MUTATED    35   8   9   1
  14Q GAIN WILD-TYPE 200  39  66   8
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               35                200
  N1                8                 39
  N2                9                 66
  N3                1                  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"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    18   2
  14Q GAIN WILD-TYPE 174   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     18    2
  14Q GAIN WILD-TYPE  174    9
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               18                174
  1                2                  9
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    22  36
  14Q GAIN WILD-TYPE  85 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     22   36
  14Q GAIN WILD-TYPE   85  265
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               22                 85
  MALE                 36                265
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    52   2
  14Q GAIN WILD-TYPE 312  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     52    2
  14Q GAIN WILD-TYPE  312   17
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                52                312
  YES                2                 17
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, continuous
D26V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         5    47
  14Q GAIN WILD-TYPE    43                        17   280
D26V12, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                 43
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                   47                280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  50
  14Q GAIN WILD-TYPE   7 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   50
  14Q GAIN WILD-TYPE    7  319
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               50                319
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    16  17
  15Q GAIN WILD-TYPE 213 160
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                373 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                17                160 
$`15Q GAIN MUTATED`
TCGA-4Z-AA7R TCGA-4Z-AA89 TCGA-BT-A20Q TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A3MH 
       17.16        29.65        19.50        28.41        23.01        13.08 
TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A2HX 
       12.00        11.34        29.79         1.84         2.14        46.68 
TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A6B1 TCGA-DK-AA6Q TCGA-E5-A4TZ TCGA-E7-A6MD 
       50.27        10.55        67.36        13.58        15.35         4.24 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EO TCGA-GC-A3BM 
       20.91         3.62         3.06        10.65        59.31        21.40 
TCGA-GC-A3I6 TCGA-GU-AATP TCGA-S5-A6DX TCGA-UY-A8OB TCGA-UY-A9PH TCGA-XF-AAMQ 
       20.71        32.98         1.84        69.34        51.32        71.57 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-ZF-A9RE 
       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 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        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-A20R TCGA-BT-A20T TCGA-BT-A20U 
       26.14        12.16        17.88         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        36.43 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        8.98         1.94        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.13        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.62        12.26        13.12        12.10        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       18.58        13.08        12.92         4.90        15.12        18.48 
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 
       17.95         7.79       142.78        87.32         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.15         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       163.30        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       76.60        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02       165.73       166.03        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 
       15.35        13.64        56.15        11.18        12.03        20.32 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        25.58         0.56         0.66        26.96        26.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       24.03        24.66         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         7.56        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-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-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-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         2.27         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        12.66        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
       11.08        61.94        48.00        15.95        26.93        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        70.32 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       29.36        15.81        19.13        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-A767 
       18.97         7.63        32.78        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       10.65         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        36.49        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        64.01         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       12.16        25.02         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        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       16.27        11.80        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       44.38         1.15        15.32        15.58        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       12.23        16.67        14.24        16.54        12.43        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       17.62        37.05        22.68        86.83        76.01        78.25 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
        3.02       112.83         3.91        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.85        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-A9SI 
       15.35         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
        3.22        15.98        66.41        34.45        14.93         4.21 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        5.98        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-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
        7.63        91.73         2.96         8.32         6.77        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        61.45        86.30        27.06        75.39        18.15 
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 
       22.36        25.41        21.11        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        28.41        94.29        13.41        64.08        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       88.87        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        56.35        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        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.84               0.10 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             71.57             166.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             20.71              16.83 
[1] "1.8 - 71.6 (20.7)"  "0.1 - 166.0 (16.8)"
[1] "hr=" "1.2"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         0       12         7       16
  15Q GAIN WILD-TYPE       2      117       133      119
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                12                117
  STAGE III                7                133
  STAGE IV                16                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
  15Q GAIN MUTATED         12  11  10
  15Q GAIN WILD-TYPE      111 184  48
D27V4, multiclass
          clus
vv         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1+T2               12                111
  T3                     11                184
  T4                     10                 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
  15Q GAIN MUTATED    20   4   8   2
  15Q GAIN WILD-TYPE 215  43  67   7
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               20                215
  N1                4                 43
  N2                8                 67
  N3                2                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    21   1
  15Q GAIN WILD-TYPE 171  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     21    1
  15Q GAIN WILD-TYPE  171   10
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               21                171
  1                1                 10
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     8  27
  15Q GAIN WILD-TYPE  99 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8   27
  15Q GAIN WILD-TYPE   99  274
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                8                 99
  MALE                 27                274
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    29   3
  15Q GAIN WILD-TYPE 335  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     29    3
  15Q GAIN WILD-TYPE  335   16
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                29                335
  YES                3                 16
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, continuous
D27V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       4                         1    28
  15Q GAIN WILD-TYPE    39                        21   299
D27V12, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                1                 21
  WHITE                                   28                299
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  31
  15Q GAIN WILD-TYPE   8 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   31
  15Q GAIN WILD-TYPE    8  338
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               31                338
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    37  37
  16P GAIN WILD-TYPE 192 140
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                74                332 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                37                140 
$`16P GAIN MUTATED`
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BT-A0S7 TCGA-BT-A20V 
       27.62         0.62        47.80         2.50         6.58         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A47X TCGA-DK-A2I2 
        8.25        17.16        28.70         8.98        12.62         7.79 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 
       13.58         8.22        50.27        21.30         9.67        66.05 
TCGA-DK-A6B2 TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA75 TCGA-E5-A2PC 
       15.68       166.03        19.00        15.35        11.18        43.59 
TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A97Q TCGA-FD-A3SJ TCGA-FD-A5BY TCGA-FD-A6TF 
       22.16        24.03         8.09        24.30         8.25         2.27 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-AA3B 
        3.06         9.67        10.65         3.25        59.31        66.02 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GD-A76B TCGA-GU-A762 TCGA-GU-AATP TCGA-GV-A3JV 
       21.40        20.71         7.36         7.63        32.98        14.27 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.40        64.01         9.01        25.02         3.45         2.76 
TCGA-K4-A83P TCGA-LC-A66R TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78M 
       16.27        15.32        14.24         1.84        38.99        22.68 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SZ 
       51.32         3.22        15.98        34.45         5.98        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        22.36        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 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       29.65        17.42        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        26.14        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB 
       19.50         5.06        14.89        14.96         8.35        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
       20.48         4.67        12.82         9.96        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         1.94        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       11.34        11.34        11.87        18.58        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
        4.90        15.12        18.48         5.19        29.79         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 
       46.68        17.95       142.78        87.32         4.80         8.15 
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       163.30        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        53.29        76.60        67.36        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T 
       38.24        52.01        15.02        13.58       165.73        18.81 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        12.03        20.32        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83        29.72         0.10         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24         4.24        24.66 
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-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-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-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
        7.56        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-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-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
        4.31        10.85        31.07        12.66        17.23         8.94 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
       11.08        61.94        48.00        15.95        26.93        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        70.32        29.36 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81        19.13        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-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 
       20.98         2.20        10.92        11.31        18.97        32.78 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW 
       20.05         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        36.49        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE 
        8.58        19.07        22.72         1.51        38.60        12.16 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         9.14        27.68         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        1.81        15.42        11.80        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       46.98        44.38         1.15        15.58        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L 
       12.23        16.67        16.54        12.43        17.62        37.05 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       86.83        76.01        78.25        69.34         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
        3.91        29.56        17.82         6.21         3.85        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-A9SL TCGA-XF-A9SP 
       17.88        48.62        64.80        79.66        66.41        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
        4.21        12.76        11.90        23.64        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH 
       18.90        16.27         2.10        13.74        92.98        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAN0 
       54.90        71.57         2.96         8.32        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        18.15 
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-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       25.41        31.20        30.28        35.84        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       94.29         3.48        64.08        58.72        88.87        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X 
       20.22         2.89        34.06        19.69         8.61        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       56.35        35.41        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.62               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            166.03             165.73 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             15.83              17.59 
[1] "0.6 - 166.0 (15.8)" "0.1 - 165.7 (17.6)"
[1] "hr=" "1.3"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         0       16        26       32
  16P GAIN WILD-TYPE       2      113       114      103
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                16                113
  STAGE III               26                114
  STAGE IV                32                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
  16P GAIN MUTATED         16  34  18
  16P GAIN WILD-TYPE      107 161  40
D28V4, multiclass
          clus
vv         16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1+T2               16                107
  T3                     34                161
  T4                     18                 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
  16P GAIN MUTATED    37  10  18   3
  16P GAIN WILD-TYPE 198  37  57   6
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               37                198
  N1               10                 37
  N2               18                 57
  N3                3                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    34   4
  16P GAIN WILD-TYPE 158   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     34    4
  16P GAIN WILD-TYPE  158    7
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               34                158
  1                4                  7
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    23  51
  16P GAIN WILD-TYPE  84 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     23   51
  16P GAIN WILD-TYPE   84  250
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               23                 84
  MALE                 51                250
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    67   3
  16P GAIN WILD-TYPE 297  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     67    3
  16P GAIN WILD-TYPE  297   16
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                67                297
  YES                3                 16
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, continuous
D28V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       4                         4    63
  16P GAIN WILD-TYPE    39                        18   264
D28V12, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   63                264
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  67
  16P GAIN WILD-TYPE   8 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   67
  16P GAIN WILD-TYPE    8  302
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               67                302
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    45  38
  16Q GAIN WILD-TYPE 184 139
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                83                323 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                38                139 
$`16Q GAIN MUTATED`
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BT-A0S7 TCGA-BT-A20R 
       27.62         0.62        47.80         2.50         6.58         5.06 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ 
        5.06         8.25        17.16        12.82        28.70         8.98 
TCGA-CF-A47X TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT 
       12.62         7.79        13.58         8.22        50.27        21.30 
TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA75 
       66.05        15.68       166.03        19.00        15.35        11.18 
TCGA-E5-A2PC TCGA-E7-A6ME TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A43P TCGA-FD-A43Y 
       43.59        24.03         8.09        32.02        27.35        15.58 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TG 
        5.36         8.25         6.28        13.35         2.27         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A3VY 
        9.67        10.85        10.65         3.25        59.31        17.62 
TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 
       66.02        21.40        20.71        24.92         8.94         7.73 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A762 TCGA-GU-AATP TCGA-GV-A3JW TCGA-H4-A2HQ 
       20.98         7.36         7.63        32.98        21.34        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6MB 
       64.01         9.01        25.02         3.45         2.76        15.42 
TCGA-LC-A66R TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A9PE 
       15.32        14.24         1.84        38.99        22.68         6.21 
TCGA-UY-A9PH TCGA-XF-A9SG TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9T3 
       51.32        48.62        15.98        34.45         5.98         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        22.36 
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 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       29.65        17.42        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        26.14        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD 
       19.50        14.89        14.96         8.35        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        4.67         9.96        17.56        36.43        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        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-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.87        18.58        13.08        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       18.48         5.19        29.79         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        46.68        17.95 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IU 
      142.78        87.32         4.80         8.15        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       163.30        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       53.29        76.60        67.36        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6W 
       52.01        15.02        13.58       165.73        18.81        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        56.15        12.03        20.32        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       29.72         0.10        22.16         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24         4.24        24.66 
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-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.37        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-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
        7.56        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       11.01        19.33         5.69        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-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
       12.36         4.31        31.07        12.66        17.23         8.94 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
       11.08        61.94        48.00        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        70.32        29.36        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I3 
       19.13        15.91        14.07        17.75         0.49        13.91 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12         2.20        10.92        11.31        18.97 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ 
       32.78        20.05         5.62         4.73        10.65         7.00 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        19.10        19.82        20.28         8.48        36.49 
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-A5NE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       12.16        21.24         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
       17.72         1.81        16.27        11.80        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT 
       35.97        46.98        44.38         1.15        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K 
       13.48        12.23        16.67        16.54        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        86.83        76.01        78.25        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB 
      112.83         3.91        29.56        17.82         3.85        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-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SP 
       17.88        64.80        79.66         3.22        66.41        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        4.21        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-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       92.98       110.60        11.31        54.90         7.63        71.57 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        2.96         8.32        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        18.15         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
        0.66        11.97        13.64        25.41        31.20        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF 
       35.84        21.86        28.41        94.29         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       58.72        88.87        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        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90         8.52        54.21         5.52        12.23 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.62               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            166.03             165.73 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             15.42              17.62 
[1] "0.6 - 166.0 (15.4)" "0.1 - 165.7 (17.6)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         0       20        32       31
  16Q GAIN WILD-TYPE       2      109       108      104
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                20                109
  STAGE III               32                108
  STAGE IV                31                104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  16Q GAIN MUTATED         19  40  17
  16Q GAIN WILD-TYPE      104 155  41
D29V4, multiclass
          clus
vv         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1+T2               19                104
  T3                     40                155
  T4                     17                 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
  16Q GAIN MUTATED    44  10  17   4
  16Q GAIN WILD-TYPE 191  37  58   5
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               44                191
  N1               10                 37
  N2               17                 58
  N3                4                  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"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    33   4
  16Q GAIN WILD-TYPE 159   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     33    4
  16Q GAIN WILD-TYPE  159    7
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               33                159
  1                4                  7
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    29  54
  16Q GAIN WILD-TYPE  78 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     29   54
  16Q GAIN WILD-TYPE   78  247
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               29                 78
  MALE                 54                247
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    73   4
  16Q GAIN WILD-TYPE 291  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     73    4
  16Q GAIN WILD-TYPE  291   15
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                73                291
  YES                4                 15
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, continuous
D29V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       4                         6    69
  16Q GAIN WILD-TYPE    39                        16   258
D29V12, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                6                 16
  WHITE                                   69                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"
D29V13, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  76
  16Q GAIN WILD-TYPE   8 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   76
  16Q GAIN WILD-TYPE    8  293
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               76                293
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    30  28
  17P GAIN WILD-TYPE 199 149
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                58                348 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                28                149 
$`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-A3MF TCGA-CF-A8HY TCGA-CU-A0YR 
       12.82        28.70         8.98        12.59        11.34        15.12 
TCGA-DK-A3IM TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA75 TCGA-FD-A3B7 
        8.15        67.36        36.66        15.02        11.18         4.01 
TCGA-FD-A3SP TCGA-FD-A5BT TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3Z7 
       25.74        11.01        12.36         2.27         4.31        31.07 
TCGA-FT-A3EE TCGA-G2-AA3F TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GV-A3JV TCGA-GV-A3QH 
        3.25        29.36         7.73         7.36        14.27         8.48 
TCGA-GV-A40E TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-LC-A66R 
        8.58        38.60         3.45        21.24         1.81        15.32 
TCGA-MV-A51V TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A9PB TCGA-XF-A8HI TCGA-XF-A9T0 
       13.48        86.83        69.34        29.56        17.88        26.27 
TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       13.74         7.63        71.57        30.28        94.29        13.41 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
       59.38        63.02        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 
       24.13        94.88       104.65       108.95         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-5N-A9KI TCGA-5N-A9KM 
       50.04        51.16        66.54        29.65         2.50        17.42 
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-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20V 
       26.14        12.16        17.88        19.50        14.89         5.06 
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-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       36.43        28.41         1.94        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       13.97        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.87        18.58        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90        18.48         5.19        29.79         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        46.68 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.95         7.79       142.78        87.32         4.80        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       163.30        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M 
       53.29        76.60        15.68        50.70        38.24        52.01 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       13.58       165.73       166.03        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       15.35        13.64        56.15        12.03        20.32        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        25.58         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
        4.24        24.03        24.66         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-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77         8.94        33.04        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-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       46.78        19.79        12.85         7.56        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-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-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        6.15        12.69         3.06         9.67        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94        11.08        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        59.31        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62        66.02         6.94        70.32        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81        19.13        15.91        14.07        17.75        24.92 
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        18.97         7.63        32.78 
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-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.10        19.82        20.28        36.49        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        64.01         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
       12.16        25.02         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       11.70        17.72        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 
       50.56        35.97        46.98        44.38         1.15        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        16.54 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       12.43        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE 
       78.25         3.02       112.83         3.91        17.82         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        3.85        51.32        45.04         6.58        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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
        3.22        15.98        66.41        34.45        14.93         4.21 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        5.98        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-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT 
       10.82       110.60        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        18.15         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        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       25.41        21.11        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        64.08        58.72        88.87        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 
        2.89        34.06        19.69         8.61        60.16        56.35 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        54.21         5.52        12.23 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.62               0.10 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             94.29             166.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            14.005             17.670 
[1] "0.6 - 94.3 (14.0)"  "0.1 - 166.0 (17.7)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED         0       16        21       20
  17P GAIN WILD-TYPE       2      113       119      115
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                16                113
  STAGE III               21                119
  STAGE IV                20                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
  17P GAIN MUTATED         15  32   6
  17P GAIN WILD-TYPE      108 163  52
D30V4, multiclass
          clus
vv         17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1+T2               15                108
  T3                     32                163
  T4                      6                 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
  17P GAIN MUTATED    30   8  13   1
  17P GAIN WILD-TYPE 205  39  62   8
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               30                205
  N1                8                 39
  N2               13                 62
  N3                1                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    24   3
  17P GAIN WILD-TYPE 168   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     24    3
  17P GAIN WILD-TYPE  168    8
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               24                168
  1                3                  8
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    15  43
  17P GAIN WILD-TYPE  92 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     15   43
  17P GAIN WILD-TYPE   92  258
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               15                 92
  MALE                 43                258
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    52   2
  17P GAIN WILD-TYPE 312  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     52    2
  17P GAIN WILD-TYPE  312   17
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                52                312
  YES                2                 17
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, continuous
D30V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       2                         3    51
  17P GAIN WILD-TYPE    41                        19   276
D30V12, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    2                 41
  BLACK OR AFRICAN AMERICAN                3                 19
  WHITE                                   51                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"
D30V13, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     2  49
  17P GAIN WILD-TYPE   7 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2   49
  17P GAIN WILD-TYPE    7  320
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               49                320
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    70  65
  17Q GAIN WILD-TYPE 159 112
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               135                271 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                65                112 
$`17Q GAIN MUTATED`
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM 
        0.62        41.75        15.12        10.22        47.80        17.42 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R 
        6.74        12.39         6.58        12.16        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A42C 
       14.89        14.96         8.35         8.25        20.48        28.70 
TCGA-C4-A0EZ TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A8HY TCGA-CU-A0YR 
        8.98        12.59        12.13        12.62        11.34        15.12 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I2 
       29.79         1.84        66.41        18.41       112.44         7.79 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 
        8.15        50.27        10.55        66.05        17.98        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA75 
       36.66        15.02        19.00        15.35        13.64        11.18 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6ME 
       43.59        22.16        25.58         0.56        26.96        24.03 
TCGA-E7-A7PW TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SP 
       13.68         8.94        33.04         4.01        24.30        25.74 
TCGA-FD-A3SQ TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA 
       46.78        26.73         5.36        58.92         7.10        62.86 
TCGA-FD-A6TB TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A3EE 
       18.81        12.36         2.27         4.31        31.07         3.25 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GU-A42P 
       70.32        29.36        21.40         7.73         7.36        10.92 
TCGA-GU-A42R TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF 
       18.97        10.65        32.98        14.27        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.48        27.35         8.58        19.07        19.40        38.60 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
        9.01        12.16         3.45        21.24         9.07        11.70 
TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V 
        1.81        11.80        46.98         1.15        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 
       69.34         3.02        29.56        97.45        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SU TCGA-XF-A9T0 
        1.87        17.88        48.62         3.22         5.98        26.27 
TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74       110.60        11.31         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M 
        2.96         8.32        56.48        86.30        11.97        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-AA4V TCGA-ZF-AA4X 
       30.28        28.41        94.29        13.41        59.38        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       35.41         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 
       24.13        11.97        94.88       104.65       108.95         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-5N-A9KI 
       27.62        50.04        51.16        66.54        29.65         2.50 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
       40.08         7.33         2.66        13.15        19.04        26.14 
TCGA-BT-A20P TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ 
       17.88         5.06        17.16        16.18         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        9.96        17.56        36.43        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       12.79        12.56        13.97        13.08        12.16        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-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.87        18.58        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        4.90        18.48         5.19        13.58        21.86         2.14 
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-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       46.68        17.95       142.78        87.32         4.80        13.58 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        17.72        21.30        23.21         9.67        20.81 
TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
      163.30        64.18        53.29        76.60        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T 
       38.24        52.01        13.58       165.73       166.03        18.81 
TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        56.15        12.03        20.32        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 
       29.72         0.10         2.24        16.70         0.66        26.24 
TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.66         0.92         1.22        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 
       15.32        14.37         8.09        32.02        16.77        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-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
        5.52        19.79        12.85         7.56        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91         3.62        15.58        53.88        11.01        19.33 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P 
        5.69         8.25        27.45        18.08         2.70         6.28 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
       13.35         6.15        12.69         3.06         9.67        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF 
       12.66        10.65        17.23         8.94        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       48.00        15.95        26.93        59.31        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        17.62        66.02         6.94        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       19.13        15.91        14.07        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        13.91         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        32.78        20.05         5.62         4.73 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.00        21.34        19.10        36.49        22.72         1.51 
TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ 
       64.01        25.02         2.76         9.14        27.68        17.72 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R 
       15.42        16.27        52.73        50.56        35.97        44.38 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 
       15.58        21.07        12.23        16.67        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD 
       38.99        17.62        78.25       112.83         3.91        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE 
        6.21         3.85        51.32        45.04         6.58       125.49 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       64.80        79.66        15.98        66.41        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        4.21        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-AAME 
       18.90         2.24        16.27        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       10.82        54.90         6.77        98.99        44.32        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        18.15         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        9.63         0.66        22.36        25.41        21.11        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       35.84        21.86         3.48        64.08        58.72        88.87 
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-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       60.16        56.35        57.90        19.40        54.21         5.52 
TCGA-ZF-AA5P 
       12.23 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.56               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            112.44             166.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             15.35              17.56 
[1] "0.6 - 112.4 (15.3)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED         0       36        43       56
  17Q GAIN WILD-TYPE       2       93        97       79
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                36                 93
  STAGE III               43                 97
  STAGE IV                56                 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
  17Q GAIN MUTATED         40  66  21
  17Q GAIN WILD-TYPE       83 129  37
D31V4, multiclass
          clus
vv         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1+T2               40                 83
  T3                     66                129
  T4                     21                 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
  17Q GAIN MUTATED    69  18  35   2
  17Q GAIN WILD-TYPE 166  29  40   7
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               69                166
  N1               18                 29
  N2               35                 40
  N3                2                  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"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    57   4
  17Q GAIN WILD-TYPE 135   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     57    4
  17Q GAIN WILD-TYPE  135    7
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               57                135
  1                4                  7
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    37  99
  17Q GAIN WILD-TYPE  70 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     37   99
  17Q GAIN WILD-TYPE   70  202
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               37                 70
  MALE                 99                202
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   126   4
  17Q GAIN WILD-TYPE 238  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    126    4
  17Q GAIN WILD-TYPE  238   15
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO               126                238
  YES                4                 15
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, continuous
D31V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED      11                         5   113
  17Q GAIN WILD-TYPE    32                        17   214
D31V12, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                   11                 32
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                  113                214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6 118
  17Q GAIN WILD-TYPE   3 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  118
  17Q GAIN WILD-TYPE    3  251
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  3
  NOT HISPANIC OR LATINO              118                251
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    66  51
  18P GAIN WILD-TYPE 163 126
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               117                289 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                51                126 
$`18P GAIN MUTATED`
TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-5N-A9KI TCGA-BL-A3JM 
       17.16         0.62        41.75        15.12         2.50         6.74 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
        5.06         8.35        16.18        28.70        36.43         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A2I2 TCGA-DK-A2I6 
        1.94        12.56        12.92        18.48         7.79        87.32 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6W 
        8.15         8.22        66.05        36.66        52.01        13.64 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A6ME TCGA-E7-A7PW TCGA-FD-A3B5 TCGA-FD-A3B6 
       11.18        15.35        24.03        13.68         8.94        33.04 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y 
       22.52        60.66        19.79        12.85        27.35        15.58 
TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 
       26.73        11.01         5.36         8.25        27.45        58.92 
TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.28        12.36         2.27         4.31        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3D 
       11.08        61.94        26.93        59.31        17.62        70.32 
TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       29.36        15.91         0.49         8.94         7.73         2.10 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-AATP 
        2.20         7.36        10.92        11.31         7.63        32.98 
TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        7.00        19.10        19.82         8.48        36.49        27.35 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ 
       19.07        19.40        12.16        21.24         9.07        17.72 
TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        11.80        46.98         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-R3-A69X TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O 
       13.48        14.24        17.62        37.05        86.83        76.01 
TCGA-UY-A9PB TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9SJ 
       29.56        51.32        45.04        97.45        15.35         3.22 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SX TCGA-XF-A9T3 TCGA-XF-AAMG 
       34.45        14.93         4.21        23.64         2.24       110.60 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY 
       54.90         7.63        71.57         2.96         6.77        98.99 
TCGA-XF-AAN0 TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4X TCGA-ZF-AA52 
       56.48        21.86        64.08        20.22        63.02        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       57.90        54.21        19.17 

$`18P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04        51.16        66.54        10.22        47.80        29.65 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 
       17.42        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        26.14        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
        5.06        14.89        14.96         8.25        17.16        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F6 
        4.67        12.82         9.96        17.56        28.41        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.79        13.97        12.59        12.13        13.08        12.16 
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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
       18.58        13.08         4.90        15.12         5.19        29.79 
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        46.68        17.95       142.78         4.80        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       163.30        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q 
       67.36        15.68        50.70        38.24        15.02        13.58 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 
      165.73       166.03        18.81        19.00        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       56.15        12.03        20.32        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        26.96        26.24         4.24        24.66         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-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SJ 
       32.02        16.77         4.01        12.62        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-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BU 
        7.56        14.96        20.91         3.62        53.88        19.33 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
        5.69        18.08         2.70         7.10        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
       18.81         6.15        12.69         3.06         9.67        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK 
       12.66        10.65         8.94         3.25        48.00        15.95 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM 
       33.01         7.23        20.12        66.02         6.94        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       20.71        15.81        19.13        14.07        17.75        24.92 
TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 
       13.91         3.12        20.98        18.97        32.78        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF 
        5.62         4.73        10.65        14.27        21.34        20.28 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        8.58        22.72         1.51        38.60        64.01         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI 
       25.02         3.45         2.76         9.14        27.68        11.70 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R 
       15.42        16.27        52.73        50.56        35.97        44.38 
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        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       38.99        22.68        78.25        69.34         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HE 
        3.91        17.82         6.21         3.85         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-A9SK TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       15.98        66.41         5.98        12.76        11.90        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-AAMF TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMW 
       13.74        92.98        10.82        11.31        91.73         8.32 
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-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        22.36        25.41        21.11        31.20        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG 
       35.84        28.41        94.29        13.41         3.48        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       88.87        47.84         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       59.38        60.16        56.35        19.40         8.52         5.52 
TCGA-ZF-AA5P 
       12.23 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.49               0.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            110.60             166.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             17.16              17.42 
[1] "0.5 - 110.6 (17.2)" "0.1 - 166.0 (17.4)"
[1] "hr=" "1"  
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         0       35        45       37
  18P GAIN WILD-TYPE       2       94        95       98
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                35                 94
  STAGE III               45                 95
  STAGE IV                37                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         31  57  17
  18P GAIN WILD-TYPE       92 138  41
D32V4, multiclass
          clus
vv         18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1+T2               31                 92
  T3                     57                138
  T4                     17                 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
  18P GAIN MUTATED    67   8  24   3
  18P GAIN WILD-TYPE 168  39  51   6
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               67                168
  N1                8                 39
  N2               24                 51
  N3                3                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    45   4
  18P GAIN WILD-TYPE 147   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     45    4
  18P GAIN WILD-TYPE  147    7
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               45                147
  1                4                  7
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    33  84
  18P GAIN WILD-TYPE  74 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     33   84
  18P GAIN WILD-TYPE   74  217
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               33                 74
  MALE                 84                217
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   104   4
  18P GAIN WILD-TYPE 260  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    104    4
  18P GAIN WILD-TYPE  260   15
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO               104                260
  YES                4                 15
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, continuous
D32V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       5                         7   101
  18P GAIN WILD-TYPE    38                        15   226
D32V12, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                7                 15
  WHITE                                  101                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"
D32V13, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3 106
  18P GAIN WILD-TYPE   6 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3  106
  18P GAIN WILD-TYPE    6  263
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              106                263
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    32  31
  18Q GAIN WILD-TYPE 197 146
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                63                343 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                31                146 
$`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        36.43 
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        36.66 
TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-FD-A3B6 TCGA-FD-A3SR 
       13.64        11.18        20.32        15.35        33.04        19.79 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TC 
       27.35        15.58        26.73         5.36        27.45         6.15 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EL TCGA-G2-A2EO 
       12.36         4.31        31.07        11.08        26.93        59.31 
TCGA-G2-AA3D TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
       70.32         8.94         2.10         7.36        10.92        11.31 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       32.98         7.00         8.48        36.49        17.72         1.81 
TCGA-LT-A5Z6 TCGA-R3-A69X TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PB 
       15.58        14.24        22.68        86.83        76.01        29.56 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SM TCGA-XF-A9ST 
       51.32        45.04        15.35        48.62        34.45         4.21 
TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RN 
        7.63        98.99        56.48        21.86        64.08        20.22 
TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA58 
       63.02        57.90        54.21 

$`18Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       47.80        29.65         2.50        17.42        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        26.14 
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-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35         8.25        17.16        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
        9.96        17.56        28.70        28.41        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       18.58        13.08        12.92         4.90        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        29.79         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-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62        46.68        17.95       142.78        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        4.80        13.58         8.15        17.72        50.27        21.30 
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       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       50.70        38.24        52.01        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        18.81        19.00        15.35        13.64        56.15 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        43.59        38.83        29.72         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        25.58         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.24         4.24        24.03        24.66         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-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-A3SS TCGA-FD-A43N TCGA-FD-A43S 
        5.52        25.74        46.78        12.85         7.56        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       20.91         3.62        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        8.25        18.08        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG 
       13.35        62.86        18.81        12.69         2.27         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85        12.66        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB 
        3.25        61.94        48.00        15.95        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        17.62        66.02         6.94        29.36        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       20.71        15.81        19.13        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       24.92         0.49        13.91         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
        2.20        18.97         7.63        32.78        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       20.28        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60        64.01         9.01        12.16        25.02 
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-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
       11.70        15.42        16.27        11.80        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT 
       35.97        46.98        44.38         1.15        15.32        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        12.23        16.67         1.84        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       38.99        17.62        37.05        78.25        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC 
      112.83         3.91        17.82         6.21         3.85         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       97.45       125.49        97.12         1.87        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9SU 
       79.66         3.22        15.98        66.41        14.93         5.98 
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-AAMZ TCGA-XF-AAN1 
       91.73         2.96         8.32         6.77        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        18.15         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        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
       25.41        21.11        31.20        30.28        35.84        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       94.29        13.41         3.48        58.72        88.87        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-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       56.35        35.41        19.40         8.52        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  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 
             17.72              17.16 
[1] "0.6 - 99.0 (17.7)"  "0.1 - 166.0 (17.2)"
[1] "hr=" "1.1"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         0       24        21       18
  18Q GAIN WILD-TYPE       2      105       119      117
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                24                105
  STAGE III               21                119
  STAGE IV                18                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
  18Q GAIN MUTATED         22  27   9
  18Q GAIN WILD-TYPE      101 168  49
D33V4, multiclass
          clus
vv         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1+T2               22                101
  T3                     27                168
  T4                      9                 49
[1] 3 2
[1] TRUE
[1] "dimension of 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    37   4  13   1
  18Q GAIN WILD-TYPE 198  43  62   8
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               37                198
  N1                4                 43
  N2               13                 62
  N3                1                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    25   1
  18Q GAIN WILD-TYPE 167  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     25    1
  18Q GAIN WILD-TYPE  167   10
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               25                167
  1                1                 10
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    17  46
  18Q GAIN WILD-TYPE  90 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     17   46
  18Q GAIN WILD-TYPE   90  255
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               17                 90
  MALE                 46                255
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    57   2
  18Q GAIN WILD-TYPE 307  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     57    2
  18Q GAIN WILD-TYPE  307   17
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                57                307
  YES                2                 17
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, continuous
D33V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       1                         2    56
  18Q GAIN WILD-TYPE    42                        20   271
D33V12, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                 42
  BLACK OR AFRICAN AMERICAN                2                 20
  WHITE                                   56                271
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  57
  18Q GAIN WILD-TYPE   7 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   57
  18Q GAIN WILD-TYPE    7  312
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               57                312
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    54  33
  19P GAIN WILD-TYPE 175 144
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                87                319 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                33                144 
$`19P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-5N-A9KI TCGA-5N-A9KM 
       16.27         0.62        51.16        15.12         2.50        17.42 
TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CF-A1HR 
        6.74        26.14         8.25        17.16         1.94        12.79 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A8HY 
       12.56        12.59        12.13        12.46        12.62        11.34 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I4 
       18.48        29.79        21.86        18.41        46.68       142.78 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-DK-AA6U 
       64.18        67.36        15.68        36.66       166.03        19.00 
TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A6MD 
       13.64        11.18        12.03        38.83         0.56         4.24 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SR TCGA-FD-A43U TCGA-FD-A43X 
       24.03         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        70.32        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        16.54        37.05        69.34         3.02         3.91 
TCGA-UY-A9PB TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI 
       29.56        51.32         6.58        97.12        15.35        79.66 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9T8 TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN5 
        5.98        12.76        13.74        44.32        56.48        75.39 
TCGA-XF-AAN7 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4T 
       18.15         9.63        21.11        64.08        20.22        19.69 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       56.35        19.40         8.52 

$`19P GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04        41.75        66.54        10.22        47.80        29.65 
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        36.43        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
        8.98        23.01        13.97        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.66        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.87        18.58        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
       15.12         5.19         1.84        13.58         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-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79        87.32         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        8.15         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       163.30        66.05        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       53.29        76.60        50.70        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 
       13.58       165.73        18.81        13.64        15.35        56.15 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       20.32        43.59        15.35        29.72         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70        25.58         0.66        26.96        26.24 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66        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-A3SS 
       17.98        29.16         5.52        25.74        46.78        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
        7.56        27.35        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-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-A6TI 
       62.86        18.81         6.15        12.69        12.36         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P 
       10.85        12.66        10.65        17.23         8.94        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        48.00        15.95        26.93        59.31        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
        7.23        20.12         6.94        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW 
       15.81        19.13        15.91        14.07        17.75         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        13.91         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        18.97         7.63        32.78        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        5.62        10.65        32.98        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        36.49        27.35         8.58        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40        64.01         9.01        12.16        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ 
       21.24         2.76         9.14        27.68        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
        1.81        15.42        16.27        11.80        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       35.97        46.98        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 
       21.07        13.48        12.23        16.67        14.24        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       38.99        17.62        22.68        86.83        76.01        78.25 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HD 
      112.83        17.82         6.21         3.85        45.04        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ 
      125.49         1.87        17.88        48.62        64.80         3.22 
TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW 
       15.98        66.41        34.45        14.93         4.21        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-AAMF TCGA-XF-AAMG 
       16.27        66.64         2.10        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-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        8.32         6.77        98.99        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       27.06         3.88        18.84         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       22.36        25.41        31.20        30.28        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL 
       28.41        94.29        13.41         3.48        58.72        88.87 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84         2.89        34.06         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       63.02        35.41        57.90        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.56               0.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            166.03             165.73 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             16.54              17.56 
[1] "0.6 - 166.0 (16.5)" "0.1 - 165.7 (17.6)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         0       27        28       31
  19P GAIN WILD-TYPE       2      102       112      104
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                27                102
  STAGE III               28                112
  STAGE IV                31                104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  19P GAIN MUTATED         25  41  16
  19P GAIN WILD-TYPE       98 154  42
D34V4, multiclass
          clus
vv         19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1+T2               25                 98
  T3                     41                154
  T4                     16                 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
  19P GAIN MUTATED    46  10  21   1
  19P GAIN WILD-TYPE 189  37  54   8
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               46                189
  N1               10                 37
  N2               21                 54
  N3                1                  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"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    41   3
  19P GAIN WILD-TYPE 151   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     41    3
  19P GAIN WILD-TYPE  151    8
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               41                151
  1                3                  8
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    20  67
  19P GAIN WILD-TYPE  87 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     20   67
  19P GAIN WILD-TYPE   87  234
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               20                 87
  MALE                 67                234
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    73   5
  19P GAIN WILD-TYPE 291  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     73    5
  19P GAIN WILD-TYPE  291   14
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                73                291
  YES                5                 14
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, continuous
D34V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED      13                         2    68
  19P GAIN WILD-TYPE    30                        20   259
D34V12, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                   13                 30
  BLACK OR AFRICAN AMERICAN                2                 20
  WHITE                                   68                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"
D34V13, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  79
  19P GAIN WILD-TYPE   8 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   79
  19P GAIN WILD-TYPE    8  290
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               79                290
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    81  53
  19Q GAIN WILD-TYPE 148 124
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               134                272 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                53                124 
$`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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V 
        2.50        17.42         6.74        19.04        26.14         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 
        8.25        17.16        16.18        28.70        36.43         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A47X 
       23.01        12.79        12.56        12.59        12.13        12.62 
TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 
       12.00        11.34        18.48        29.79        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL 
       18.41        16.70        46.68       142.78        87.32        13.58 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L 
       66.05        64.18        67.36        15.68        36.66        38.24 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 
       15.02       166.03        19.00        13.64        11.18        12.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6MD 
       43.59        15.35        38.83        25.58         0.56         4.24 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS 
       24.03         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 
        7.56        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        59.31        17.62        66.02        70.32        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        18.97         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-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K 
       35.97        46.98        14.24         1.84        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PH 
       37.05        69.34         3.02         3.91        29.56        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SK 
       45.04         6.58        97.12        15.35        79.66        15.98 
TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9T3 TCGA-XF-AAMQ TCGA-XF-AAMX 
       14.93         5.98        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        18.15         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA51 
       13.64        21.11        88.87        20.22        19.69        56.35 
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 
       24.13        11.97        94.88       104.65       108.95         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        50.04 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        47.80        29.65        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-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       13.97        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.10        12.26        13.12        12.10        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
       18.58        13.08        12.92         4.90        15.12         5.19 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD 
        1.84        13.58         2.14        19.00       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK 
       16.14        17.62        15.62        17.95         7.79         4.80 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        8.15         8.22        17.72        50.27        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       163.30        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T 
       76.60        50.70        52.01        13.58       165.73        18.81 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.64        15.35        56.15        20.32        29.72         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       22.16         2.24        16.70         0.66        26.96        26.24 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66        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-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-A43P TCGA-FD-A43S 
       29.16         5.52        25.74        46.78        27.35        14.96 
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-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        13.35        62.86         6.15        12.69        12.36 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EJ 
        9.67        12.66        10.65         8.94        11.08        48.00 
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-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC 
       29.36        21.40        20.71        15.81        19.13        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-A762 TCGA-GU-A763 TCGA-GU-A764 
        2.20        10.92        11.31         7.63        32.78        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        5.62        10.65        19.10         8.48        36.49        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE 
        8.58        19.07        22.72         1.51        64.01        12.16 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ 
        3.45        21.24         9.14        27.68        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
        1.81        15.42        16.27        11.80        52.73        50.56 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       44.38         1.15        15.32        15.58        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N 
       12.23        16.67        12.43        38.99        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       76.01        78.25       112.83        17.82         6.21         3.85 
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-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX 
        3.22        66.41        34.45         4.21        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-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-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY 
       54.90         7.63        91.73         2.96         8.32        98.99 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A9TC 
       30.94        61.45        27.06         3.88        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       11.97        22.36        25.41        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        94.29        13.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84         2.89        34.06         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       60.16        63.02        35.41        57.90        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.56               0.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            166.03             165.73 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            17.620             16.735 
[1] "0.6 - 166.0 (17.6)" "0.1 - 165.7 (16.7)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         0       36        44       53
  19Q GAIN WILD-TYPE       2       93        96       82
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                36                 93
  STAGE III               44                 96
  STAGE IV                53                 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
  19Q GAIN MUTATED         35  64  23
  19Q GAIN WILD-TYPE       88 131  35
D35V4, multiclass
          clus
vv         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1+T2               35                 88
  T3                     64                131
  T4                     23                 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
  19Q GAIN MUTATED    69  17  32   4
  19Q GAIN WILD-TYPE 166  30  43   5
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               69                166
  N1               17                 30
  N2               32                 43
  N3                4                  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    60   5
  19Q GAIN WILD-TYPE 132   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     60    5
  19Q GAIN WILD-TYPE  132    6
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               60                132
  1                5                  6
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    35  99
  19Q GAIN WILD-TYPE  72 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     35   99
  19Q GAIN WILD-TYPE   72  202
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               35                 72
  MALE                 99                202
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   118   4
  19Q GAIN WILD-TYPE 246  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    118    4
  19Q GAIN WILD-TYPE  246   15
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO               118                246
  YES                4                 15
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, continuous
D35V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED      13                         5   108
  19Q GAIN WILD-TYPE    30                        17   219
D35V12, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                   13                 30
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                  108                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"
D35V13, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3 119
  19Q GAIN WILD-TYPE   6 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3  119
  19Q GAIN WILD-TYPE    6  250
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              119                250
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   110  90
  20P GAIN WILD-TYPE 119  87
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               200                206 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                90                 87 
$`20P GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7S 
       24.13        11.97       108.95        16.27        44.94        34.98 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
        0.62        41.75        66.54        10.22        47.80         2.50 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
        6.74         6.58         5.06        14.89         5.06         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        36.43        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF 
        8.98         1.94        23.01        12.79        12.56        12.59 
TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47X TCGA-CF-A8HX TCGA-CU-A0YN 
       12.13        12.16        12.66        12.62        11.34        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1AC 
        4.90        15.12        18.48         1.84         2.14       130.88 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
      112.44        46.68        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B1 
       13.58         8.22        23.21        10.55        17.98        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6U 
       15.68        36.66        38.24        15.02       165.73        19.00 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A2PC TCGA-E5-A4TZ 
       15.35        13.64        56.15        11.18        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q 
       38.83        25.58        24.03         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         7.56 
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        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       48.00        15.95        59.31        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.81        19.13        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        36.49        19.07        19.40 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ 
       12.16        25.02         3.45         9.07        11.70         1.81 
TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41S TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        50.56        35.97         1.15        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M 
       16.67         1.84        12.43        38.99        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE 
       76.01        69.34         3.02         3.91        29.56         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        3.85        51.32        97.45        97.12        15.35         1.87 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SU 
       79.66         3.22        15.98        34.45        14.93         5.98 
TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAMF 
       12.76        21.04         2.24        16.27        66.64        10.82 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-YC-A89H 
       71.57        91.73         2.96        98.99        44.32        18.84 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        22.36        25.41        21.11        31.20        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       94.29        88.87        47.84        20.22         2.89        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 
        8.61        59.38        56.35        35.41        19.40        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       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 
       94.88       104.65         8.35        16.83        16.77        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-5N-A9KM 
       27.62        50.04        51.16        15.12        29.65        17.42 
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-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LA 
       26.14        12.16        17.88        19.50        14.96        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A3MH 
       16.18         4.67        12.82        17.56        13.97        13.08 
TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       10.95        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.87        18.58        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       29.79        13.58        21.86        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IM 
       16.70        16.14        17.62        15.62        87.32         8.15 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       17.72        50.27        21.30         9.67        20.81       163.30 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6M 
       66.05        64.18        53.29        76.60        50.70        52.01 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA76 TCGA-DK-AA77 
       13.58       166.03        18.81        13.64        12.03        20.32 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         0.10        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        26.96        26.24         4.24        24.66         0.92 
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-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43S 
       12.62        27.98        17.98        29.16         5.52        14.96 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       20.91        15.58        53.88        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA 
        8.25        18.08        58.92         2.70         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
       18.81         3.06        31.07        12.66        17.23         8.94 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       26.93        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OQ TCGA-GD-A3OS 
        6.94        70.32        17.75        24.92         3.12        20.98 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 
       10.92        11.31        18.97         7.63        32.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE 
        7.00        27.35         8.58        22.72         1.51        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       64.01         9.01        21.24         2.76         9.14        27.68 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-KQ-A41R 
       17.72        15.42        16.27        52.73        46.98        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-AA26 TCGA-UY-A78K 
       15.32        15.58        21.07        14.24        16.54        17.62 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC 
       86.83        78.25       112.83        17.82        45.04         6.58 
TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9ST 
      125.49        17.88        48.62        64.80        66.41         4.21 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T6 
       11.90        23.64        28.24        26.27        18.90         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-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        8.32         6.77        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.15         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       11.97        35.84        21.86        28.41        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4R TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA53 
       64.08        58.72        34.06        60.16        63.02        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA5P 
        8.52        12.23 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.49               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            165.73             166.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             15.93              17.62 
[1] "0.5 - 165.7 (15.9)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.1"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         0       58        67       76
  20P GAIN WILD-TYPE       2       71        73       59
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                58                 71
  STAGE III               67                 73
  STAGE IV                76                 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         54 100  32
  20P GAIN WILD-TYPE       69  95  26
D36V4, multiclass
          clus
vv         20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1+T2               54                 69
  T3                    100                 95
  T4                     32                 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
  20P GAIN MUTATED   106  26  40   8
  20P GAIN WILD-TYPE 129  21  35   1
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              106                129
  N1               26                 21
  N2               40                 35
  N3                8                  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    86   8
  20P GAIN WILD-TYPE 106   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     86    8
  20P GAIN WILD-TYPE  106    3
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               86                106
  1                8                  3
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    53 148
  20P GAIN WILD-TYPE  54 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     53  148
  20P GAIN WILD-TYPE   54  153
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               53                 54
  MALE                148                153
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   181   6
  20P GAIN WILD-TYPE 183  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    181    6
  20P GAIN WILD-TYPE  183   13
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               181                183
  YES                6                 13
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, continuous
D36V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED      12                        10   172
  20P GAIN WILD-TYPE    31                        12   155
D36V12, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                   12                 31
  BLACK OR AFRICAN AMERICAN               10                 12
  WHITE                                  172                155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 183
  20P GAIN WILD-TYPE   7 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  183
  20P GAIN WILD-TYPE    7  186
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO              183                186
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   125 103
  20Q GAIN WILD-TYPE 104  74
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               228                178 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               103                 74 
$`20Q GAIN MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       24.13        11.97       104.65       108.95        16.27        44.94 
TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KI 
       34.98         0.62        41.75        66.54        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q 
       17.42         6.74         6.58        19.04        26.14        19.50 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35         8.25        20.48         9.96        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         8.98         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.56        12.59        12.13        12.16        10.95        12.66 
TCGA-CF-A47X TCGA-CF-A8HX TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       12.62        11.34        12.92         4.90        15.12        18.48 
TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD 
        1.84         2.14        66.41        18.41       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM 
       46.68        17.95         7.79       142.78        13.58         8.15 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6AV 
        8.22        50.27        23.21        10.55        17.98        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6R 
       67.36        15.68        36.66        38.24        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        19.00        13.64        15.35        13.64        56.15 
TCGA-DK-AA75 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 
       11.18        43.59        15.35        38.83        22.16        25.58 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 
       24.03         1.22        13.68        12.95         8.09        32.02 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP 
       33.04         4.01        22.52        60.66        24.30        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X 
       46.78        19.79        12.85         7.56        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
       26.73        11.01        27.45        18.08        58.92         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-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P 
        9.67        10.85        31.07        10.65         3.25        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B 
       61.94        48.00        15.95        59.31        17.62        66.02 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       70.32        29.36        21.40        20.71        15.81        19.13 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        24.92         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A766 
        7.73         2.10         7.36        11.31        18.97         5.62 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       10.65        32.98        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-H4-A2HQ TCGA-HQ-A2OE 
       20.28         8.48        36.49         8.58        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RH 
       64.01        12.16        25.02         3.45         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41S 
       11.70         1.81        11.80        50.56        35.97         1.15 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-SY-A9G0 
       15.58        13.48        12.23        16.67         1.84        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
        3.02         3.91        29.56         6.21         3.85        51.32 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SI 
       45.04        97.45        97.12        15.35         1.87        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         5.98        12.76 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       23.64        21.04         2.24        16.27        66.64         2.10 
TCGA-XF-AAMF TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY 
       10.82        71.57        91.73         2.96         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
       44.32        30.94        13.64        22.36        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RG 
       31.20        30.28        21.86        94.29        13.41        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       88.87        47.84        20.22         2.89        19.69         8.61 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       56.35        35.41        19.40        54.21        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 
       94.88         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 
       50.04        51.16        15.12        10.22        29.65        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-A3MH TCGA-CF-A47V TCGA-CF-A47W 
       12.82        17.56        13.97        13.08        12.46        12.10 
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-A9FL TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
       18.58        13.08         5.19        29.79        13.58        21.86 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 
       19.00        16.70        16.14        17.62        15.62        87.32 
TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        4.80        17.72        21.30         9.67        20.81       163.30 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6Q 
       66.05        53.29        76.60        50.70        52.01        13.58 
TCGA-DK-AA6T TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       18.81        12.03        20.32        29.72         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 
       24.66         0.92        14.07        15.32        14.37        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        8.94        12.62        27.98        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU 
        5.52        14.96        20.91        15.58        53.88        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA 
        5.36         5.69         8.25         2.70         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EL 
       18.81         3.06        12.66        17.23         8.94        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3WC TCGA-GD-A3OQ 
       33.01         7.23        20.12         6.94        17.75         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       20.98         2.20        10.92         7.63        32.78        20.05 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.73         7.00        27.35        19.07        22.72         1.51 
TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB 
        9.01        21.24         2.76        27.68        17.72        15.42 
TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A8JT 
       16.27        52.73        46.98        44.38        15.32        21.07 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
       14.24        16.54        86.83        78.25       112.83        17.82 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL 
        6.58       125.49        17.88        48.62        64.80        66.41 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T8 
        4.21        11.90        28.24        26.27        18.90        13.74 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMW 
       92.98       110.60        11.31        54.90         7.63         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        61.45        86.30        27.06        75.39        18.15 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 
        3.88        18.84         9.63         0.66        11.97        35.84 
TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4W 
       28.41         3.48        64.08        34.06        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA5P 
       63.02        57.90         8.52        12.23 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.49               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            166.03             163.30 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            17.785             16.800 
[1] "0.5 - 166.0 (17.8)" "0.1 - 163.3 (16.8)"
[1] "hr=" "1"  
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         0       68        78       82
  20Q GAIN WILD-TYPE       2       61        62       53
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                68                 61
  STAGE III               78                 62
  STAGE IV                82                 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         63 113  34
  20Q GAIN WILD-TYPE       60  82  24
D37V4, multiclass
          clus
vv         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1+T2               63                 60
  T3                    113                 82
  T4                     34                 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
  20Q GAIN MUTATED   123  26  47   8
  20Q GAIN WILD-TYPE 112  21  28   1
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              123                112
  N1               26                 21
  N2               47                 28
  N3                8                  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   99  7
  20Q GAIN WILD-TYPE 93  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     99    7
  20Q GAIN WILD-TYPE   93    4
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               99                 93
  1                7                  4
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    65 164
  20Q GAIN WILD-TYPE  42 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     65  164
  20Q GAIN WILD-TYPE   42  137
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               65                 42
  MALE                164                137
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   203  10
  20Q GAIN WILD-TYPE 161   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    203   10
  20Q GAIN WILD-TYPE  161    9
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               203                161
  YES               10                  9
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, continuous
D37V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED      17                         9   190
  20Q GAIN WILD-TYPE    26                        13   137
D37V12, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                   17                 26
  BLACK OR AFRICAN AMERICAN                9                 13
  WHITE                                  190                137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3 206
  20Q GAIN WILD-TYPE   6 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  206
  20Q GAIN WILD-TYPE    6  163
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              206                163
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    69  46
  21Q GAIN WILD-TYPE 160 131
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               115                291 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                46                131 
$`21Q GAIN MUTATED`
TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA81 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W 
       94.88        16.27        41.75        12.39        26.14         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-A3MG TCGA-CF-A47V TCGA-CF-A8HY TCGA-CF-A9FL 
       12.56        13.97        12.13        12.46        11.34        18.58 
TCGA-CU-A3KJ TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 
       18.48        21.86        18.41        17.95       142.78        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 
        4.80        13.58         8.15        50.27         9.67        66.05 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U 
       17.98        67.36        15.68        15.02       166.03        19.00 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A97Q 
       11.18        15.35        22.16        24.03        13.68         8.09 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP 
       33.04         4.01        60.66        24.30        29.16        25.74 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P 
       19.79         7.56        27.45        18.08         7.10         6.28 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-G2-A2EF 
        6.15        12.36         3.06         4.31        17.23        61.94 
TCGA-G2-A2EK TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A4ZW TCGA-GC-A6I3 
       15.95        17.62        66.02        21.40         0.49        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF 
        7.73         2.10        10.92        21.34        19.10        20.28 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A6FZ TCGA-K4-A6MB 
        8.58        19.07        19.40         3.45         1.81        15.42 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-SY-A9G5 
       35.97        46.98         1.15        15.32        13.48        38.99 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
       22.68        86.83         3.02         6.21         3.85        51.32 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP 
       97.45        97.12         1.87         3.22        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY 
        4.21         5.98        28.24        91.73         6.77        98.99 
TCGA-XF-AAMZ TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL 
       44.32        13.64        25.41        30.28        94.29        88.87 
TCGA-ZF-A9RM TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA52 
       47.84        19.69         8.61        59.38        56.35        35.41 
TCGA-ZF-AA5P 
       12.23 

$`21Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97       104.65       108.95         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        50.04 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       29.65         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       16.18         4.67        12.82        17.56        36.43        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       23.01        12.79        12.59        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        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-A0YO 
       12.10        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
       15.12         5.19        29.79         1.84        13.58         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IN TCGA-DK-A3IQ 
       17.62        15.62        46.68         7.79         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV 
       21.30        23.21        20.81        10.55       163.30        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       53.29        76.60        50.70        36.66        38.24        52.01 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       165.73        18.81        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       56.15        12.03        20.32        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         2.24        16.70        25.58         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.96        26.24         4.24        24.66         0.92         1.22 
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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM 
        8.94        12.62        22.52        27.98        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
        5.52        46.78        12.85        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-A5C1 TCGA-FD-A62N TCGA-FD-A62S 
        5.36         5.69         8.25        58.92         2.70        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK 
       62.86        18.81        12.69         2.27         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       31.07        12.66        10.65         8.94         3.25        11.08 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        26.93        59.31        33.01         7.23        20.12 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        70.32        29.36        20.71        15.81        19.13 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ 
       15.91        14.07        17.75        24.92         8.94         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       20.98         2.20         7.36        11.31        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       32.78        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        7.00        14.27        19.82         8.48        36.49        27.35 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       22.72         1.51        38.60        64.01         9.01        12.16 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
       25.02        21.24         2.76         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
       11.70        17.72        16.27        11.80        52.73        50.56 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       44.38        15.58        21.07        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O 
        1.84        16.54        12.43        17.62        37.05        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       78.25        69.34       112.83         3.91        29.56        17.82 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SG 
       45.04         6.58       125.49        15.35        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW 
       64.80        79.66        15.98        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 
       18.15         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 
       22.36        21.11        31.20        35.84        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        64.08        58.72        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 
       54.21        19.17         5.52 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.49               0.10 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            166.03             165.73 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             17.95              16.77 
[1] "0.5 - 166.0 (17.9)" "0.1 - 165.7 (16.8)"
[1] "hr=" "1.2"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         0       33        41       41
  21Q GAIN WILD-TYPE       2       96        99       94
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                33                 96
  STAGE III               41                 99
  STAGE IV                41                 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
  21Q GAIN MUTATED         30  61  13
  21Q GAIN WILD-TYPE       93 134  45
D38V4, multiclass
          clus
vv         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1+T2               30                 93
  T3                     61                134
  T4                     13                 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
  21Q GAIN MUTATED    60  12  26   2
  21Q GAIN WILD-TYPE 175  35  49   7
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               60                175
  N1               12                 35
  N2               26                 49
  N3                2                  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    52   3
  21Q GAIN WILD-TYPE 140   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     52    3
  21Q GAIN WILD-TYPE  140    8
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               52                140
  1                3                  8
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    25  90
  21Q GAIN WILD-TYPE  82 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     25   90
  21Q GAIN WILD-TYPE   82  211
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               25                 82
  MALE                 90                211
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED   101   4
  21Q GAIN WILD-TYPE 263  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    101    4
  21Q GAIN WILD-TYPE  263   15
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO               101                263
  YES                4                 15
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, continuous
D38V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED      11                         4    96
  21Q GAIN WILD-TYPE    32                        18   231
D38V12, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                   11                 32
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   96                231
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2 107
  21Q GAIN WILD-TYPE   7 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2  107
  21Q GAIN WILD-TYPE    7  262
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO              107                262
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    23  26
  22Q GAIN WILD-TYPE 206 151
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                49                357 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                26                151 
$`22Q GAIN MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-5N-A9KM TCGA-BT-A0S7 TCGA-BT-A20W 
      104.65        44.94        34.98        17.42         6.58         8.35 
TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-CF-A8HY TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I6 
       16.18        12.82        11.34        66.41       112.44        87.32 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-AA77 TCGA-E7-A4IJ TCGA-E7-A541 
       50.27        23.21        10.55        20.32        22.16        25.58 
TCGA-FD-A3B7 TCGA-FD-A62O TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM 
        4.01         7.10        59.31        33.01        70.32        21.40 
TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JZ 
       20.71        14.07         0.49         4.73        14.27        19.82 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A2OE TCGA-KQ-A41P 
        8.48        36.49        27.35         8.58        38.60        35.97 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78O TCGA-XF-A9SI 
       44.38        15.58         1.84        12.43        76.01        79.66 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-ZF-A9R0 
        7.63        71.57        91.73         8.32         6.77        22.36 
TCGA-ZF-A9R4 
       30.28 

$`22Q GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97        94.88       108.95         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        50.04         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-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       29.65         2.50        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        26.14        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       17.16        20.48         4.67         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         8.98         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
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-A9FF TCGA-CF-A9FL 
       13.12        12.00        12.10        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90        15.12        18.48         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
       29.79         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 
       46.68        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
        8.15         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 
      163.30        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       67.36        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       15.02        13.58       165.73       166.03        18.81        19.00 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 
       13.64        15.35        13.64        56.15        11.18        12.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       43.59        15.35        38.83        29.72         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       24.03        24.66         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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
        8.94        33.04        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         7.56        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-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-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        12.66        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        11.08        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS 
       29.36        15.81        19.13        15.91        17.75        24.92 
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        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       32.78        20.05         5.62        10.65        32.98         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       21.34        19.10        20.28        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40        64.01         9.01        12.16        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-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V 
       50.56        46.98         1.15        15.32        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       12.23        16.67        14.24        16.54        38.99        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        78.25        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
      112.83         3.91        29.56        17.82         6.21         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       51.32        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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU 
       15.98        66.41        34.45        14.93         4.21         5.98 
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-AAMT 
       92.98        10.82       110.60        11.31        54.90         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-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.15         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        25.41        21.11        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       35.84        21.86        28.41        94.29        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       64.08        58.72        88.87        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 
       56.35        35.41        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        12.23 

  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 
             21.40              16.77 
[1] "0.5 - 112.4 (21.4)" "0.1 - 166.0 (16.8)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED         0       18        17       13
  22Q GAIN WILD-TYPE       2      111       123      122
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                18                111
  STAGE III               17                123
  STAGE IV                13                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
  22Q GAIN MUTATED         18  21   7
  22Q GAIN WILD-TYPE      105 174  51
D39V4, multiclass
          clus
vv         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1+T2               18                105
  T3                     21                174
  T4                      7                 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
  22Q GAIN MUTATED    29   4   7   3
  22Q GAIN WILD-TYPE 206  43  68   6
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               29                206
  N1                4                 43
  N2                7                 68
  N3                3                  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   1
  22Q GAIN WILD-TYPE 166  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     26    1
  22Q GAIN WILD-TYPE  166   10
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               26                166
  1                1                 10
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    12  37
  22Q GAIN WILD-TYPE  95 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     12   37
  22Q GAIN WILD-TYPE   95  264
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               12                 95
  MALE                 37                264
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    46   2
  22Q GAIN WILD-TYPE 318  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     46    2
  22Q GAIN WILD-TYPE  318   17
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                46                318
  YES                2                 17
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, continuous
D39V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       3                         3    41
  22Q GAIN WILD-TYPE    40                        19   286
D39V12, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    3                 40
  BLACK OR AFRICAN AMERICAN                3                 19
  WHITE                                   41                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"
D39V13, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  43
  22Q GAIN WILD-TYPE   9 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   43
  22Q GAIN WILD-TYPE    9  326
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               43                326
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    37  29
  XP GAIN WILD-TYPE 192 148
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               66               340 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               29               148 
$`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 
       26.14        17.88        19.50        16.18        28.70        12.56 
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 
       22.16        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        20.71 
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        36.49        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        69.34 
TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9T5 
        3.02        17.82         3.85         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        18.15        11.97        21.11        64.08        59.38 

$`XP GAIN WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04        51.16        66.54        15.12        10.22        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ 
        2.50        17.42        40.08         7.33         2.66        12.39 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       13.15        19.04        12.16         5.06        14.89        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-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        17.56        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
        1.94        23.01        12.79        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       18.58        13.08        12.92         4.90        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        29.79         1.84        13.58        21.86         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG 
       18.41        19.00        16.70       112.44        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       46.68        17.95         7.79       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         8.15         8.22        17.72        50.27        21.30 
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       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q 
       50.70        36.66        38.24        52.01        15.02        13.58 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
      165.73       166.03        18.81        19.00        13.64        15.35 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       56.15        11.18        12.03        20.32        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83        29.72         0.10         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66         0.92         1.22        14.07        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-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-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
        7.56        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-A62O TCGA-FD-A62P 
       27.45        18.08        58.92         2.70         7.10         6.28 
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-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        3.06         4.31        10.85        12.66        10.65         8.94 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       11.08        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D 
       33.01         7.23        20.12        17.62         6.94        70.32 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       29.36        21.40        15.81        19.13        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 
       17.75        24.92         0.49         2.10         3.12         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        7.36        11.31        18.97         7.63        32.78        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        5.62        10.65         7.00        14.27        21.34        19.10 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       20.28        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       19.40        64.01        12.16        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        2.76         9.14         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
       15.42        16.27        11.80        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       46.98        44.38         1.15        15.32        15.58        21.07 
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        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA 
       38.99        37.05        86.83        78.25       112.83         3.91 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       29.56         6.21        51.32        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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
        3.22        15.98        66.41        34.45        14.93         4.21 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        5.98        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-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       10.82        54.90         7.63        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-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        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       25.41        31.20        30.28        35.84        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       94.29        13.41         3.48        58.72        88.87        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W 
       20.22         2.89        34.06        19.69         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        56.35        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21        19.17         5.52        12.23 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.62              0.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           130.88            166.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           17.720            16.995 
[1] "0.6 - 130.9 (17.7)" "0.1 - 166.0 (17.0)"
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP GAIN MUTATED         0       18        24       23
  XP GAIN WILD-TYPE       2      111       116      112
D40V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               18               111
  STAGE III              24               116
  STAGE IV               23               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
  XP GAIN MUTATED         20  32   9
  XP GAIN WILD-TYPE      103 163  49
D40V4, multiclass
          clus
vv         XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1+T2              20               103
  T3                    32               163
  T4                     9                49
[1] 3 2
[1] TRUE
[1] "dimension of 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 198  37  63   7
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              37               198
  N1              10                37
  N2              12                63
  N3               2                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    28   0
  XP GAIN WILD-TYPE 164  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     28    0
  XP GAIN WILD-TYPE  164   11
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              28               164
  1               0                11
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    20  46
  XP GAIN WILD-TYPE  87 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     20   46
  XP GAIN WILD-TYPE   87  255
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              20                87
  MALE                46               255
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    61   0
  XP GAIN WILD-TYPE 303  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     61    0
  XP GAIN WILD-TYPE  303   19
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               61               303
  YES               0                19
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, continuous
D40V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       8                         5    49
  XP GAIN WILD-TYPE    35                        17   278
D40V12, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   8                35
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                  49               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"
D40V13, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     3  54
  XP GAIN WILD-TYPE   6 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3   54
  XP GAIN WILD-TYPE    6  315
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO              54               315
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    24  23
  XQ GAIN WILD-TYPE 205 154
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               47               359 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               23               154 
$`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        26.14 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A42C TCGA-CF-A1HS TCGA-CF-A5UA TCGA-CF-A8HX 
       17.88        19.50        28.70        12.56        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        20.71         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        69.34         3.02         6.58 
TCGA-XF-A9SM TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ 
       34.45        66.64        13.74        11.31         7.63        71.57 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9R2 TCGA-ZF-AA4V 
        6.77        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 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04         0.62        51.16        66.54        15.12        10.22 
TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       29.65         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20T 
       12.39        13.15        19.04        12.16         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-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
       20.48         4.67        12.82         9.96        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       28.41         8.98         1.94        23.01        12.79        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       18.48         5.19        29.79         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62        46.68        17.95         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         4.80        13.58         8.15         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-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
      163.30        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P 
       67.36        15.68        50.70        36.66        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       13.58       165.73       166.03        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 
       15.35        13.64        56.15        11.18        12.03        20.32 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       43.59        15.35        38.83        29.72         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        25.58         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.24         4.24        24.03        24.66         0.92         1.22 
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-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-A43S 
       25.74        46.78        19.79        12.85         7.56        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-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK 
       18.81        12.69        12.36         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        12.66        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 
       11.08        61.94        48.00        15.95        26.93        59.31 
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-A3RC 
       70.32        29.36        21.40        15.81        19.13        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP 
       14.07        17.75        24.92         0.49        13.91         2.10 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12         2.20         7.36        10.92        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        32.78        20.05         5.62         4.73        10.65 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10        20.28        36.49 
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-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60        64.01        12.16        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        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
        1.81        15.42        16.27        11.80        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       35.97        46.98        44.38         1.15        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        16.54 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78P 
       12.43        38.99        17.62        37.05        86.83        78.25 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
      112.83         3.91        29.56        17.82         6.21         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
       51.32        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-A9SK TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       15.98        66.41        14.93         4.21         5.98        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-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
        2.24        16.27         2.10        92.98        10.82       110.60 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 
       54.90        91.73         2.96         8.32        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        18.15         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        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       25.41        31.20        30.28        35.84        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       94.29        13.41         3.48        64.08        58.72        88.87 
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        56.35        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21        19.17         5.52        12.23 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             2.27              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            98.99            166.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            17.88             17.16 
[1] "2.3 - 99.0 (17.9)"  "0.1 - 166.0 (17.2)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         0       13        18       16
  XQ GAIN WILD-TYPE       2      116       122      119
D41V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               13               116
  STAGE III              18               122
  STAGE IV               16               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
  XQ GAIN MUTATED         13  25   6
  XQ GAIN WILD-TYPE      110 170  52
D41V4, multiclass
          clus
vv         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1+T2              13               110
  T3                    25               170
  T4                     6                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
  XQ GAIN MUTATED    28   8   7   1
  XQ GAIN WILD-TYPE 207  39  68   8
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              28               207
  N1               8                39
  N2               7                68
  N3               1                 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"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    19   1
  XQ GAIN WILD-TYPE 173  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     19    1
  XQ GAIN WILD-TYPE  173   10
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              19               173
  1               1                10
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    14  33
  XQ GAIN WILD-TYPE  93 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     14   33
  XQ GAIN WILD-TYPE   93  268
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              14                93
  MALE                33               268
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    44   0
  XQ GAIN WILD-TYPE 320  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     44    0
  XQ GAIN WILD-TYPE  320   19
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               44               320
  YES               0                19
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, continuous
D41V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       6                         3    36
  XQ GAIN WILD-TYPE    37                        19   291
D41V12, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   6                37
  BLACK OR AFRICAN AMERICAN               3                19
  WHITE                                  36               291
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  40
  XQ GAIN WILD-TYPE   8 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   40
  XQ GAIN WILD-TYPE    8  329
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              40               329
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    16  18
  1P LOSS WILD-TYPE 213 159
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34               372 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               18               159 
$`1P LOSS MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A3PK TCGA-CF-A47X 
       24.13         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        15.12        17.72        21.30        36.66        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-KQ-A41P TCGA-PQ-A6FI TCGA-S5-A6DX 
       32.98        64.01        25.02        35.97        12.23         1.84 
TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       17.62        76.01       112.83        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-AAN2 TCGA-ZF-A9R3 TCGA-ZF-A9RL 
       15.98        61.45        31.20        88.87 

$`1P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        94.88       104.65       108.95         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 
       50.04        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM 
       47.80        29.65         2.50        17.42         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        26.14        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-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82        17.56        28.70        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        1.94        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ 
       11.34        11.87        18.58        13.08        12.92        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        29.79         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        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      142.78        87.32         4.80        13.58         8.15         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       163.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       66.05        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R 
       15.68        50.70        38.24        52.01        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        18.81        19.00        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       56.15        11.18        20.32        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
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         7.56        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-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-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-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       31.07        12.66        17.23         8.94         3.25        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        48.00        15.95        26.93        59.31        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        70.32 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       29.36        21.40        20.71        15.81        19.13        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-GD-A76B 
        7.73         2.10         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        18.97         7.63        32.78        20.05 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        4.73        10.65         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        36.49        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND 
       19.07        22.72         1.51        19.40        38.60         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       12.16         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        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       11.80        52.73        50.56        46.98        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        21.07        13.48        16.67        14.24 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       16.54        12.43        38.99        37.05        22.68        86.83 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       78.25        69.34         3.02         3.91        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
        6.21         3.85        51.32        45.04         6.58        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-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       66.41        34.45        14.93         4.21         5.98        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-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        30.94        86.30        27.06        75.39        18.15 
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-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       22.36        25.41        21.11        30.28        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        94.29        13.41         3.48        64.08        58.72 
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        56.35        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        54.21        19.17         5.52        12.23 

  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 
           16.800            17.195 
[1] "0.6 - 112.8 (16.8)" "0.1 - 166.0 (17.2)"
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         1       13         6       14
  1P LOSS WILD-TYPE       1      116       134      121
D42V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               13               116
  STAGE III               6               134
  STAGE IV               14               121
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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  13   2
  1P LOSS WILD-TYPE      109 182  56
D42V4, multiclass
          clus
vv         1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1+T2              14               109
  T3                    13               182
  T4                     2                56
[1] 3 2
[1] TRUE
[1] "dimension of 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   4   8   2
  1P LOSS WILD-TYPE 219  43  67   7
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              16               219
  N1               4                43
  N2               8                67
  N3               2                 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   2
  1P LOSS WILD-TYPE 179   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     13    2
  1P LOSS WILD-TYPE  179    9
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              13               179
  1               2                 9
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     7  27
  1P LOSS WILD-TYPE 100 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      7   27
  1P LOSS WILD-TYPE  100  274
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               7               100
  MALE                27               274
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    31   2
  1P LOSS WILD-TYPE 333  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     31    2
  1P LOSS WILD-TYPE  333   17
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               31               333
  YES               2                17
[1] 2 2
[1] FALSE
D42V9, continuous
D42V10, continuous
D42V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         1    31
  1P LOSS WILD-TYPE    42                        21   296
D42V12, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                42
  BLACK OR AFRICAN AMERICAN               1                21
  WHITE                                  31               296
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  32
  1P LOSS WILD-TYPE   9 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   32
  1P LOSS WILD-TYPE    9  337
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              32               337
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    15  19
  1Q LOSS WILD-TYPE 214 158
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               34               372 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               19               158 
$`1Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A3PK TCGA-CU-A0YO 
       24.13         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 
       46.68        17.72        21.30        66.05        36.66        13.58 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TE 
       12.03        43.59        22.16         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-KQ-A41P TCGA-S5-A6DX TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A8HC 
       35.97         1.84        17.62        76.01       112.83         6.58 
TCGA-XF-A8HF TCGA-XF-AAN2 TCGA-ZF-A9R3 TCGA-ZF-A9RL 
       97.12        61.45        31.20        88.87 

$`1Q LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        94.88       104.65       108.95         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 
       50.04        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM 
       47.80        29.65         2.50        17.42         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        26.14        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-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82        17.56        28.70        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        1.94        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       11.34        11.34        11.87        18.58        13.08        12.92 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       15.12        18.48         5.19        29.79         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-A2I1 
      130.88       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       142.78        87.32         4.80        13.58         8.15 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        50.27        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 
      163.30        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R 
       15.68        50.70        38.24        52.01        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        18.81        19.00        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       56.15        11.18        20.32        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         2.24        16.70        25.58         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU 
       26.96        26.24         4.24        24.03        24.66         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-A43U TCGA-FD-A43X 
       12.85         7.56        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-A5BV 
       15.58        26.73        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-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF 
        7.10        62.86        18.81         6.15        12.69         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        12.66 
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        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       48.00        15.95        26.93        59.31        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        70.32        29.36        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       20.71        15.81        19.13        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-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        32.78         4.73        10.65         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.10        19.82        20.28        36.49        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 
       64.01         9.01        12.16        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        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
        1.81        15.42        16.27        11.80        52.73        50.56 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       46.98        44.38         1.15        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        12.23        16.67        14.24        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB 
       38.99        37.05        22.68        86.83        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
        3.02         3.91        29.56        17.82         6.21         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
       51.32        45.04        97.45       125.49        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       17.88        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       66.41        34.45        14.93         4.21         5.98        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-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        30.94        86.30        27.06        75.39        18.15 
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-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       22.36        25.41        21.11        30.28        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        94.29        13.41         3.48        64.08        58.72 
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        56.35        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        54.21        19.17         5.52        12.23 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.62              0.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           112.83            166.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           20.085            16.800 
[1] "0.6 - 112.8 (20.1)" "0.1 - 166.0 (16.8)"
[1] "hr=" "1.2"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED         1       16         5       12
  1Q LOSS WILD-TYPE       1      113       135      123
D43V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               16               113
  STAGE III               5               135
  STAGE IV               12               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
  1Q LOSS MUTATED         14  12   2
  1Q LOSS WILD-TYPE      109 183  56
D43V4, multiclass
          clus
vv         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1+T2              14               109
  T3                    12               183
  T4                     2                56
[1] 3 2
[1] TRUE
[1] "dimension of 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   1
  1Q LOSS WILD-TYPE 220  44  67   8
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              15               220
  N1               3                44
  N2               8                67
  N3               1                 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   1
  1Q LOSS WILD-TYPE 178  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14    1
  1Q LOSS WILD-TYPE  178   10
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              14               178
  1               1                10
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9  25
  1Q LOSS WILD-TYPE  98 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   25
  1Q LOSS WILD-TYPE   98  276
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               9                98
  MALE                25               276
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    32   0
  1Q LOSS WILD-TYPE 332  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     32    0
  1Q LOSS WILD-TYPE  332   19
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               32               332
  YES               0                19
[1] 2 2
[1] FALSE
D43V9, continuous
D43V10, continuous
D43V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       2                         2    30
  1Q LOSS WILD-TYPE    41                        20   297
D43V12, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   2                41
  BLACK OR AFRICAN AMERICAN               2                20
  WHITE                                  30               297
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  33
  1Q LOSS WILD-TYPE   9 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   33
  1Q LOSS WILD-TYPE    9  336
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              33               336
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    27  18
  2P LOSS WILD-TYPE 202 159
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               45               361 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               18               159 
$`2P LOSS MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N 
        8.35        34.98         2.50        40.08         2.66        26.14 
TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A2HX TCGA-DK-A3IS 
       12.59        12.16        18.48         5.19        46.68        50.27 
TCGA-DK-A3IV TCGA-E5-A4U1 TCGA-E7-A7DU TCGA-E7-A7PW TCGA-FD-A3B5 TCGA-FD-A3SJ 
        9.67        38.83         0.92        13.68         8.94        24.30 
TCGA-FD-A5BR TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3YS 
       26.73        10.65        26.93        66.02        15.81        24.92 
TCGA-GC-A4ZW TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-HQ-A5NE TCGA-K4-A3WU 
        0.49        10.65        14.27        21.34        12.16         3.45 
TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-KQ-A41S TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A9PF 
       17.72        11.80         1.15        13.48        16.54         3.85 
TCGA-XF-A8HH TCGA-XF-A9SV TCGA-XF-AAMF TCGA-XF-AAMT TCGA-YF-AA3M TCGA-ZF-A9RG 
        1.87        12.76        10.82         2.96        13.64        58.72 
TCGA-ZF-A9RM TCGA-ZF-AA4X TCGA-ZF-AA5H 
       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 
       24.13        11.97        94.88       104.65       108.95        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        50.04 
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-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       47.80        29.65        17.42         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-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        36.43        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH 
       23.01        12.79        12.56        13.97        12.13        13.08 
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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL 
       18.58        13.08        12.92         4.90        15.12        29.79 
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-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62        17.95         7.79       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         8.15         8.22        17.72        21.30        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       163.30        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S 
       38.24        52.01        15.02        13.58       165.73       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       18.81        19.00        13.64        15.35        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       11.18        12.03        20.32        43.59        15.35        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
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-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-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        60.66        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         7.56        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-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-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-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        4.31         9.67        10.85        31.07        12.66        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        11.08        61.94        48.00        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       59.31        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 
       70.32        29.36        21.40        20.71        19.13        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-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 
       18.97         7.63        32.78        20.05         5.62         4.73 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       32.98         7.00        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       36.49        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV 
       19.40        38.60        64.01         9.01        25.02        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ 
        2.76         9.14        27.68         9.07        11.70         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       15.42        16.27        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       44.38        15.32        15.58        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        12.43        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       22.68        86.83        76.01        78.25        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PH 
      112.83         3.91        29.56        17.82         6.21        51.32 
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-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       17.88        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW 
       66.41        34.45        14.93         4.21         5.98        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-AAMG 
       16.27        66.64         2.10        13.74        92.98       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW 
       11.31        54.90         7.63        71.57        91.73         8.32 
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-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.15         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        22.36        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       31.20        30.28        35.84        21.86        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41         3.48        64.08        88.87        20.22         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        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       35.41        57.90        19.40         8.52        54.21         5.52 
TCGA-ZF-AA5P 
       12.23 

  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 
            13.64             17.62 
[1] "0.5 - 66.0 (13.6)"  "0.1 - 166.0 (17.6)"
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         1       13        16       15
  2P LOSS WILD-TYPE       1      116       124      120
D44V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               13               116
  STAGE III              16               124
  STAGE IV               15               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
  2P LOSS MUTATED         15  19   8
  2P LOSS WILD-TYPE      108 176  50
D44V4, multiclass
          clus
vv         2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1+T2              15               108
  T3                    19               176
  T4                     8                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
  2P LOSS MUTATED    22   4  10   1
  2P LOSS WILD-TYPE 213  43  65   8
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              22               213
  N1               4                43
  N2              10                65
  N3               1                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    22   2
  2P LOSS WILD-TYPE 170   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     22    2
  2P LOSS WILD-TYPE  170    9
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              22               170
  1               2                 9
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9  36
  2P LOSS WILD-TYPE  98 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9   36
  2P LOSS WILD-TYPE   98  265
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               9                98
  MALE                36               265
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    37   4
  2P LOSS WILD-TYPE 327  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     37    4
  2P LOSS WILD-TYPE  327   15
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               37               327
  YES               4                15
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, continuous
D44V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       3                         3    35
  2P LOSS WILD-TYPE    40                        19   292
D44V12, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   3                40
  BLACK OR AFRICAN AMERICAN               3                19
  WHITE                                  35               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"
D44V13, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  40
  2P LOSS WILD-TYPE   8 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   40
  2P LOSS WILD-TYPE    8  329
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              40               329
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    50  41
  2Q LOSS WILD-TYPE 179 136
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               91               315 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               41               136 
$`2Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-5N-A9KI TCGA-BL-A0C8 
       24.13        94.88         8.35        34.98         2.50        40.08 
TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH 
        2.66        26.14        14.89         5.06        17.16         4.67 
TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A7I0 
        8.98        12.56        12.59        12.16        12.62        12.10 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A2HX TCGA-DK-A3IK TCGA-DK-A3IS 
       12.92        18.48         5.19        46.68         4.80        50.27 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6R 
        9.67        17.98        64.18        67.36        36.66       165.73 
TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A97P 
       20.32        38.83        25.58         0.92        13.68        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A5BR 
        8.09        16.77         8.94        24.30        19.79        26.73 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
        5.36        27.45         2.70        12.36         2.27         4.31 
TCGA-FT-A61P TCGA-G2-A2EL TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW 
       11.08        26.93        66.02        15.81        14.07         0.49 
TCGA-GD-A3OP TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QK TCGA-HQ-A2OE 
        2.10        10.65        14.27        21.34        27.35        38.60 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-KQ-A41P 
       12.16         3.45         9.14        17.72        11.80        35.97 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78N 
       44.38         1.15        15.58        13.48        16.54        86.83 
TCGA-UY-A9PD TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-AAMF 
       17.82        15.35         1.87        14.93        12.76        10.82 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-YF-AA3L TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R9 
      110.60         2.96        11.97        21.11        31.20        28.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4X TCGA-ZF-AA53 
       64.08        58.72        47.84        20.22        63.02        57.90 
TCGA-ZF-AA5H 
       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       104.65       108.95        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        50.04         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        29.65 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42         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-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         8.25        16.18        20.48        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
       17.56        28.70        36.43        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       12.79        13.97        12.13        13.08        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX 
       12.46        12.10        12.26        13.12        12.00        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       29.79         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-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62        17.95         7.79       142.78        87.32 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         8.15         8.22        17.72        21.30        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81        10.55       163.30        66.05        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        50.70        38.24        52.01        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        18.81        19.00        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       56.15        11.18        12.03        43.59        15.35        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV 
       26.96        26.24         4.24        24.03        24.66         1.22 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 
       14.07        12.95        15.32        32.02        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-A3SS TCGA-FD-A43N 
       29.16         5.52        25.74        46.78        12.85         7.56 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        15.58        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-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-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       12.69         3.06         9.67        10.85        31.07        12.66 
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        48.00 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       15.95        59.31        33.01         7.23        20.12        17.62 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB 
        6.94        70.32        29.36        21.40        20.71        19.13 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.91        17.75        24.92         8.94        13.91         7.73 
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 
       18.97         7.63        32.78        20.05         5.62         4.73 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       32.98         7.00        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       36.49         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
       64.01         9.01        25.02        21.24         2.76        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N 
        9.07        11.70         1.81        15.42        16.27        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       50.56        46.98        15.32        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        12.43        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       22.68        76.01        78.25        69.34         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
        3.91        29.56         6.21         3.85        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SG 
        6.58        97.45       125.49        97.12        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
       64.80        79.66         3.22        15.98        66.41        34.45 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        4.21         5.98        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-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        92.98        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-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.15 
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        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       25.41        30.28        35.84        21.86        94.29        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
        3.48        88.87         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       59.38        60.16        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21         5.52        12.23 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.49              0.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           165.73            166.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            15.58             17.62 
[1] "0.5 - 165.7 (15.6)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         1       28        29       32
  2Q LOSS WILD-TYPE       1      101       111      103
D45V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               28               101
  STAGE III              29               111
  STAGE IV               32               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
  2Q LOSS MUTATED         30  41  16
  2Q LOSS WILD-TYPE       93 154  42
D45V4, multiclass
          clus
vv         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1+T2              30                93
  T3                    41               154
  T4                    16                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
  2Q LOSS MUTATED    44   9  22   2
  2Q LOSS WILD-TYPE 191  38  53   7
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              44               191
  N1               9                38
  N2              22                53
  N3               2                 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    45   4
  2Q LOSS WILD-TYPE 147   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     45    4
  2Q LOSS WILD-TYPE  147    7
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              45               147
  1               4                 7
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    25  66
  2Q LOSS WILD-TYPE  82 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     25   66
  2Q LOSS WILD-TYPE   82  235
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              25                82
  MALE                66               235
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    78   6
  2Q LOSS WILD-TYPE 286  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     78    6
  2Q LOSS WILD-TYPE  286   13
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               78               286
  YES               6                13
[1] 2 2
[1] FALSE
D45V9, continuous
D45V10, continuous
D45V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       9                         5    71
  2Q LOSS WILD-TYPE    34                        17   256
D45V12, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                  71               256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  83
  2Q LOSS WILD-TYPE   7 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   83
  2Q LOSS WILD-TYPE    7  286
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              83               286
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    25  28
  3P LOSS WILD-TYPE 204 149
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               53               353 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               28               149 
$`3P LOSS MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA7R TCGA-4Z-AA82 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20V 
      104.65        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        12.56        12.00 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A2I2 TCGA-DK-A3IM 
       12.92        18.48        66.41        16.70         7.79         8.15 
TCGA-DK-A3WX TCGA-DK-A6B5 TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA75 TCGA-E7-A4IJ 
       10.55        50.70        13.58       165.73        11.18        22.16 
TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A43Y TCGA-FD-A5C1 
        1.22        16.77        33.04        22.52        15.58        58.92 
TCGA-G2-A3IB TCGA-G2-AA3B TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A767 
        7.23        66.02        19.13        17.75        24.92         4.73 
TCGA-K4-A4AC TCGA-K4-A5RI TCGA-UY-A78O TCGA-XF-A8HD TCGA-XF-A9T0 TCGA-XF-A9T5 
        9.14        11.70        76.01        97.45        26.27        66.64 
TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9RE 
       71.57         2.96         8.32        86.30        13.64         3.48 
TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5H 
       58.72        20.22        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 
       24.13        11.97        94.88       108.95         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        50.04 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       29.65         2.50        17.42         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        26.14        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-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-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF 
       36.43        28.41        23.01        12.79        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        29.79         1.84        13.58        21.86         2.14 
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-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62        46.68        17.95       142.78        87.32         4.80 
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       163.30        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L 
       53.29        76.60        67.36        15.68        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       52.01        15.02       166.03        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       15.35        13.64        56.15        12.03        20.32        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        29.72         0.10         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       25.58         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       24.03        24.66         0.92        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 
       15.32        14.37         8.09        32.02         8.94         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.62        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 
        7.56        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        12.66 
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        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31        33.01        20.12 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62         6.94        70.32        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.81        15.91        14.07         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         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        18.97         7.63        32.78        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62        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        36.49        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 
       64.01         9.01        12.16        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.76        27.68         9.07        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       16.27        11.80        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       44.38         1.15        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        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P 
       38.99        17.62        37.05        22.68        86.83        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       69.34         3.02       112.83         3.91        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE 
        6.21         3.85        51.32        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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       79.66         3.22        15.98        66.41        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        4.21         5.98        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       28.24        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-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 
       91.73         6.77        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        18.15         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        22.36        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       31.20        30.28        35.84        21.86        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R 
       13.41        64.08        88.87        47.84         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        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40        54.21         5.52        12.23 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.22              0.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           165.73            166.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            17.16             17.23 
[1] "1.2 - 165.7 (17.2)" "0.1 - 166.0 (17.2)"
[1] "hr=" "1.2"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         1       13        19       20
  3P LOSS WILD-TYPE       1      116       121      115
D46V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               13               116
  STAGE III              19               121
  STAGE IV               20               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
  3P LOSS MUTATED         14  25  11
  3P LOSS WILD-TYPE      109 170  47
D46V4, multiclass
          clus
vv         3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1+T2              14               109
  T3                    25               170
  T4                    11                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
  3P LOSS MUTATED    29   7   9   2
  3P LOSS WILD-TYPE 206  40  66   7
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              29               206
  N1               7                40
  N2               9                66
  N3               2                 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"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    27   1
  3P LOSS WILD-TYPE 165  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     27    1
  3P LOSS WILD-TYPE  165   10
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              27               165
  1               1                10
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    23  30
  3P LOSS WILD-TYPE  84 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     23   30
  3P LOSS WILD-TYPE   84  271
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              23                84
  MALE                30               271
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    49   2
  3P LOSS WILD-TYPE 315  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     49    2
  3P LOSS WILD-TYPE  315   17
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               49               315
  YES               2                17
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, continuous
D46V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       3                         6    40
  3P LOSS WILD-TYPE    40                        16   287
D46V12, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   3                40
  BLACK OR AFRICAN AMERICAN               6                16
  WHITE                                  40               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"
D46V13, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  46
  3P LOSS WILD-TYPE   8 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   46
  3P LOSS WILD-TYPE    8  323
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              46               323
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    13  11
  3Q LOSS WILD-TYPE 216 166
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               24               382 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               11               166 
$`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-DK-AA75 TCGA-E7-A7DV 
       12.92        10.55        50.70        13.58        11.18         1.22 
TCGA-FD-A43Y TCGA-FD-A5C1 TCGA-G2-AA3B TCGA-GU-A767 TCGA-K4-A4AC TCGA-UY-A78O 
       15.58        58.92        66.02         4.73         9.14        76.01 
TCGA-XF-A8HD TCGA-XF-A9T0 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-AA4W TCGA-ZF-AA5H 
       97.45        26.27        28.41        58.72        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 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I 
       10.22        47.80        29.65         2.50        17.42         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        26.14 
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        36.43 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
       28.41        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       18.48         5.19        29.79         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        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       142.78        87.32         4.80        13.58         8.15 
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       163.30        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       76.60        67.36        15.68        36.66        38.24        52.01 
TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02       165.73       166.03        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       15.35        13.64        56.15        12.03        20.32        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        25.58         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN 
        4.24        24.03        24.66         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-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         7.56        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        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-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07        12.66        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        11.08        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        59.31        33.01         7.23        20.12        17.62 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        70.32        29.36        21.40        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       19.13        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        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       32.78        20.05         5.62        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-GV-A6ZA TCGA-H4-A2HO 
       36.49        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60        64.01         9.01        12.16        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45        21.24         2.76        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       50.56        35.97        46.98        44.38         1.15        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        16.54        12.43        38.99        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        78.25        69.34         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
        3.91        29.56        17.82         6.21         3.85        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58       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-A9SK 
       17.88        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       66.41        34.45        14.93         4.21         5.98        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-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-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        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-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       30.94        61.45        86.30        27.06        75.39        18.15 
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 
       22.36        25.41        21.11        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL 
       21.86        94.29        13.41         3.48        64.08        88.87 
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-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       59.38        63.02        56.35        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21         5.52        12.23 

  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 
           16.370            17.325 
[1] "1.2 - 97.5 (16.4)"  "0.1 - 166.0 (17.3)"
[1] "hr=" "1"  
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         1        5         9        9
  3Q LOSS WILD-TYPE       1      124       131      126
D47V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II                5               124
  STAGE III               9               131
  STAGE IV                9               126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  3Q LOSS MUTATED          6  13   5
  3Q LOSS WILD-TYPE      117 182  53
D47V4, multiclass
          clus
vv         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1+T2               6               117
  T3                    13               182
  T4                     5                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
  3Q LOSS MUTATED    15   2   5   1
  3Q LOSS WILD-TYPE 220  45  70   8
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              15               220
  N1               2                45
  N2               5                70
  N3               1                 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"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    12   1
  3Q LOSS WILD-TYPE 180  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     12    1
  3Q LOSS WILD-TYPE  180   10
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              12               180
  1               1                10
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     8  16
  3Q LOSS WILD-TYPE  99 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      8   16
  3Q LOSS WILD-TYPE   99  285
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               8                99
  MALE                16               285
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    22   1
  3Q LOSS WILD-TYPE 342  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     22    1
  3Q LOSS WILD-TYPE  342   18
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               22               342
  YES               1                18
[1] 2 2
[1] FALSE
D47V9, continuous
D47V10, continuous
D47V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         1    20
  3Q LOSS WILD-TYPE    42                        21   307
D47V12, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                42
  BLACK OR AFRICAN AMERICAN               1                21
  WHITE                                  20               307
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  21
  3Q LOSS WILD-TYPE   9 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   21
  3Q LOSS WILD-TYPE    9  348
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              21               348
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    70  73
  4P LOSS WILD-TYPE 159 104
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              143               263 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               73               104 
$`4P LOSS MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 
       24.13        16.77        17.16        27.62         0.62        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J 
       15.12        10.22         2.50        40.08         2.66        19.04 
TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB 
       26.14         5.06         5.06         8.35         8.25        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS 
       20.48         4.67        17.56        36.43        12.79        12.56 
TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CU-A0YN TCGA-CU-A0YO TCGA-DK-A1A7 TCGA-DK-A1AD 
       12.13        12.16        12.92         4.90        18.41       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN 
       46.68        17.95        87.32         4.80         8.15         8.22 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       21.30         9.67        17.98        15.68        50.70        36.66 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-E5-A4TZ TCGA-E7-A3X6 
       13.58       165.73       166.03        13.64        15.35        29.72 
TCGA-E7-A4IJ TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL 
       22.16        32.02         8.94        33.04         4.01        23.41 
TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BY 
        5.52        12.85         7.56        26.73        19.33         8.25 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TG 
       58.92         2.70         7.10         6.28        13.35         3.06 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3IB TCGA-G2-AA3F TCGA-GC-A3BM 
        4.31        31.07        17.23         7.23        29.36        21.40 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 
       15.81        19.13        24.92        13.91         7.73         2.20 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A40G 
       11.31         7.63        20.05        32.98        14.27        19.07 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R 
       19.40        64.01        25.02        21.24         9.14        27.68 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P 
       11.70        17.72        15.42        11.80        50.56        35.97 
TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
        1.15        12.23        16.67        14.24         1.84        16.54 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD 
       12.43        38.99        17.62        22.68        69.34       112.83 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG 
       29.56         6.21         3.85         6.58        97.12        15.35 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T5 
        3.22        15.98         4.21        23.64        21.04        66.64 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 
      110.60        54.90         2.96        44.32        56.48        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       86.30        18.15        13.64        22.36        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN 
       94.29        13.41         3.48        64.08        58.72        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA53 
        2.89        19.69        60.16        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        94.88       104.65       108.95         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        50.04        41.75        66.54 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       47.80        29.65        17.42         7.33         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
        6.58        13.15        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F 
       14.96        17.16        12.82         9.96        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH 
        8.98         1.94        23.01        13.97        12.59        13.08 
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-A9FL TCGA-CF-A9FM TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       18.58        13.08        15.12        18.48         5.19        29.79 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
        1.84        13.58        21.86         2.14        66.41        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-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WW 
      142.78        13.58        17.72        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       163.30        66.05        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
       67.36        38.24        52.01        15.02        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 
       15.35        13.64        56.15        11.18        12.03        20.32 
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        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       24.66         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.32        14.37         8.09        16.77        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP 
       27.98        60.66        24.30        17.98        29.16        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       46.78        19.79        27.35        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ 
       15.58        53.88        11.01         5.36         5.69        27.45 
TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       18.08        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        2.27         9.67        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        11.08        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       59.31        33.01        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW 
       70.32        20.71        15.91        14.07        17.75         0.49 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
        8.94         2.10         3.12        20.98         7.36        10.92 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ 
       18.97        32.78         5.62         4.73        10.65         7.00 
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        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND 
       27.35         8.58        22.72         1.51        38.60         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A83P 
       12.16         3.45         2.76         9.07         1.81        16.27 
TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       52.73        46.98        44.38        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       13.48        37.05        86.83        76.01        78.25         3.02 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
        3.91        17.82        51.32        45.04        97.45       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ 
       34.45        14.93         5.98        12.76        11.90        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-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       92.98        10.82        11.31         7.63        71.57        91.73 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
        8.32         6.77        98.99        30.94        27.06        75.39 
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        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RL TCGA-ZF-A9RM 
       21.11        31.20        30.28        35.84        88.87        47.84 
TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
       34.06         8.61        59.38        56.35        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21        19.17         5.52        12.23 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.62              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           166.03            163.30 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            17.56             16.83 
[1] "0.6 - 166.0 (17.6)" "0.1 - 163.3 (16.8)"
[1] "hr=" "1.3"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         1       35        43       64
  4P LOSS WILD-TYPE       1       94        97       71
D48V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               35                94
  STAGE III              43                97
  STAGE IV               64                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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  78  20
  4P LOSS WILD-TYPE       87 117  38
D48V4, multiclass
          clus
vv         4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1+T2              36                87
  T3                    78               117
  T4                    20                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
  4P LOSS MUTATED    62  23  37   2
  4P LOSS WILD-TYPE 173  24  38   7
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              62               173
  N1              23                24
  N2              37                38
  N3               2                 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    60   4
  4P LOSS WILD-TYPE 132   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     60    4
  4P LOSS WILD-TYPE  132    7
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              60               132
  1               4                 7
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    35 108
  4P LOSS WILD-TYPE  72 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     35  108
  4P LOSS WILD-TYPE   72  193
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              35                72
  MALE               108               193
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   127   6
  4P LOSS WILD-TYPE 237  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    127    6
  4P LOSS WILD-TYPE  237   13
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              127               237
  YES               6                13
[1] 2 2
[1] FALSE
D48V9, continuous
D48V10, continuous
D48V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       9                        13   117
  4P LOSS WILD-TYPE    34                         9   210
D48V12, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN              13                 9
  WHITE                                 117               210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     4 127
  4P LOSS WILD-TYPE   5 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4  127
  4P LOSS WILD-TYPE    5  242
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             127               242
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    72  64
  4Q LOSS WILD-TYPE 157 113
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              136               270 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               64               113 
$`4Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA84 
      108.95        16.77        17.16         0.62        51.16        15.12 
TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20R 
       10.22         2.50        40.08         2.66        26.14         5.06 
TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        5.06        16.18        20.48         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI 
       28.41         1.94        12.79        12.56        12.13        12.16 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 
       12.92         4.90        15.12       112.44        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT 
        7.79        87.32         4.80         8.15         8.22        21.30 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6R 
       64.18        15.68        50.70        36.66        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B3 
      166.03        13.64        15.35        25.58         0.92        32.02 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43Y 
       33.04         4.01        23.41         5.52         7.56        15.58 
TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
       26.73         8.25        27.45        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.28        13.35         3.06         4.31        31.07        17.23 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB 
       61.94        26.93         7.23        21.40        15.81        19.13 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 
       13.91         7.73         2.20        11.31         7.63        20.05 
TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS 
       32.98        14.27        19.07        19.40        64.01        25.02 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       21.24         9.14        27.68        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-MV-A51V 
       15.42        50.56        35.97        46.98         1.15        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       12.23        16.67        14.24        12.43        38.99        17.62 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE 
       22.68        86.83        69.34       112.83        29.56         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SX 
        3.85        51.32         6.58        97.12        15.35        23.64 
TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW 
       21.04        66.64       110.60        54.90         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R4 
       56.48        61.45        86.30        13.64        22.36        30.28 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        94.29        13.41         3.48        64.08        58.72 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA54 
        2.89        19.69        63.02        19.40 

$`4Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97        94.88       104.65         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        50.04        41.75 
TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM 
       66.54        47.80        29.65        17.42         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-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-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C 
       12.82         9.96        28.70         8.98        23.01        13.97 
TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.59        13.08        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-A9FL TCGA-CF-A9FM TCGA-CU-A3KJ TCGA-CU-A3QU 
       11.34        11.87        18.58        13.08        18.48         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       29.79         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
       15.62       142.78        13.58        17.72        50.27        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       163.30        66.05        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       53.29        76.60        67.36        38.24        52.01        15.02 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       18.81        19.00        15.35        13.64        56.15        11.18 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        20.32        43.59        38.83        29.72         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW 
       26.24         4.24        24.03        24.66         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 
       14.07        12.95        15.32        14.37         8.09        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        8.94        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       17.98        29.16        25.74        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35        14.96        20.91         3.62        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB 
       19.33         5.36         5.69        18.08        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK 
        6.15        12.69        12.36         2.27         9.67        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        11.08        48.00 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       15.95        59.31        33.01        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        70.32        29.36        20.71        15.91        14.07 
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-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 
       20.98         7.36        10.92        18.97        32.78         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        10.65         7.00        21.34        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        36.49        27.35         8.58        22.72 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB 
        1.51        38.60         9.01        12.16         3.45         2.76 
TCGA-K4-A5RH TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41R TCGA-LC-A66R 
        9.07        16.27        11.80        52.73        44.38        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78O 
       15.58        21.07         1.84        16.54        37.05        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HD 
       78.25         3.02         3.91        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-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
        3.22        15.98        66.41        34.45        14.93         4.21 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
        5.98        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-AAMX TCGA-XF-AAMY 
       11.31         7.63        71.57        91.73         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        27.06        75.39        18.15         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        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       31.20        35.84        28.41        88.87        47.84        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
       34.06         8.61        59.38        60.16        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90         8.52        54.21        19.17         5.52        12.23 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.62              0.10 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           166.03            163.30 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           17.395            16.995 
[1] "0.6 - 166.0 (17.4)" "0.1 - 163.3 (17.0)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         1       35        44       56
  4Q LOSS WILD-TYPE       1       94        96       79
D49V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               35                94
  STAGE III              44                96
  STAGE IV               56                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
  4Q LOSS MUTATED         37  70  19
  4Q LOSS WILD-TYPE       86 125  39
D49V4, multiclass
          clus
vv         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1+T2              37                86
  T3                    70               125
  T4                    19                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
  4Q LOSS MUTATED    67  20  31   2
  4Q LOSS WILD-TYPE 168  27  44   7
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              67               168
  N1              20                27
  N2              31                44
  N3               2                 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    58   4
  4Q LOSS WILD-TYPE 134   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     58    4
  4Q LOSS WILD-TYPE  134    7
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              58               134
  1               4                 7
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    36 100
  4Q LOSS WILD-TYPE  71 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     36  100
  4Q LOSS WILD-TYPE   71  201
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              36                71
  MALE               100               201
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   119   6
  4Q LOSS WILD-TYPE 245  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    119    6
  4Q LOSS WILD-TYPE  245   13
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              119               245
  YES               6                13
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, continuous
D49V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       9                        10   112
  4Q LOSS WILD-TYPE    34                        12   215
D49V12, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN              10                12
  WHITE                                 112               215
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     4 120
  4Q LOSS WILD-TYPE   5 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4  120
  4Q LOSS WILD-TYPE    5  249
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             120               249
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    29  26
  5P LOSS WILD-TYPE 200 151
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               55               351 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               26               151 
$`5P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-BL-A0C8 TCGA-BL-A13J 
       24.13         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-CF-A3MI TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IL 
       12.79        12.16        18.41       112.44        17.95        13.58 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-AA75 TCGA-E5-A2PC 
        8.15        50.27        21.30        66.05        11.18        43.59 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43U 
       24.03         0.92        33.04        24.30        23.41        20.91 
TCGA-FD-A5BZ TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A3VY TCGA-GC-A6I1 TCGA-GD-A6C6 
       27.45        10.65        61.94        17.62         8.94         2.20 
TCGA-GV-A3JW TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       21.34        22.72         9.01         3.45        21.24         2.76 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-R3-A69X TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PF 
       52.73        35.97        14.24       112.83        17.82         3.85 
TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SV TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 
       15.35        79.66        12.76         6.77        44.32        56.48 
TCGA-ZF-A9R0 
       22.36 

$`5P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       11.97        94.88       104.65       108.95        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        50.04         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        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
        2.50        17.42         7.33         6.74        12.39        13.15 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       26.14        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-A3PJ 
       14.96         5.06         8.35         8.25        17.16        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        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
        1.94        12.56        13.97        12.59        12.13        13.08 
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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       18.58        13.08        12.92         4.90        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        29.79         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        46.68         7.79       142.78        87.32         4.80 
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 
      163.30        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       15.68        50.70        36.66        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       13.58       165.73       166.03        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ 
       15.35        13.64        56.15        12.03        20.32        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         0.10        22.16         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       25.58         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       24.66         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-A3SM TCGA-FD-A3SN 
       12.62        22.52        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         7.56 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        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-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-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        4.31         9.67        10.85        31.07        12.66        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        11.08        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       59.31        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 
       70.32        29.36        21.40        20.71        15.81        19.13 
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-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-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        18.97         7.63        32.78        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX 
        4.73        10.65        32.98         7.00        14.27        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        36.49        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       19.07         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       25.02         9.14        27.68         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41Q 
        1.81        15.42        16.27        11.80        50.56        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       44.38         1.15        15.32        15.58        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       12.23        16.67         1.84        16.54        12.43        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       17.62        37.05        22.68        86.83        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PH 
       69.34         3.02         3.91        29.56         6.21        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
       45.04         6.58        97.45       125.49        97.12         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL 
       17.88        48.62        64.80         3.22        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX 
       34.45        14.93         4.21         5.98        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-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
        8.32        98.99        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        18.15         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       11.97        13.64        25.41        21.11        31.20        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       35.84        21.86        28.41        94.29        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       64.08        58.72        88.87        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 
       56.35        35.41        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        12.23 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.92              0.10 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           112.83            166.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            18.41             16.70 
[1] "0.9 - 112.8 (18.4)" "0.1 - 166.0 (16.7)"
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         1       14        20       21
  5P LOSS WILD-TYPE       1      115       120      114
D50V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               14               115
  STAGE III              20               120
  STAGE IV               21               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
  5P LOSS MUTATED         15  29   9
  5P LOSS WILD-TYPE      108 166  49
D50V4, multiclass
          clus
vv         5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1+T2              15               108
  T3                    29               166
  T4                     9                49
[1] 3 2
[1] TRUE
[1] "dimension of 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    30   5  12   3
  5P LOSS WILD-TYPE 205  42  63   6
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              30               205
  N1               5                42
  N2              12                63
  N3               3                 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    27   4
  5P LOSS WILD-TYPE 165   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     27    4
  5P LOSS WILD-TYPE  165    7
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              27               165
  1               4                 7
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    16  40
  5P LOSS WILD-TYPE  91 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     16   40
  5P LOSS WILD-TYPE   91  261
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              16                91
  MALE                40               261
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    51   2
  5P LOSS WILD-TYPE 313  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     51    2
  5P LOSS WILD-TYPE  313   17
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               51               313
  YES               2                17
[1] 2 2
[1] FALSE
D50V9, continuous
D50V10, continuous
D50V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       5                         4    45
  5P LOSS WILD-TYPE    38                        18   282
D50V12, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   5                38
  BLACK OR AFRICAN AMERICAN               4                18
  WHITE                                  45               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"
D50V13, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1  50
  5P LOSS WILD-TYPE   8 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   50
  5P LOSS WILD-TYPE    8  319
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              50               319
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    83  75
  5Q LOSS WILD-TYPE 146 102
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              158               248 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               75               102 
$`5Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       24.13        11.97       108.95        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-CF-A3MH TCGA-CU-A3QU TCGA-DK-A1A5 
       36.43        23.01        12.79        13.08         5.19         2.14 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
      112.44        17.95        13.58         8.15         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6B2 
       50.27        21.30        23.21        10.55        66.05        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U 
       50.70        15.02        13.58       165.73       166.03        19.00 
TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       13.64        11.18        12.03        43.59        15.35        29.72 
TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 
       22.16        24.03         0.92        13.68         8.09         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       33.04        22.52        24.30        23.41        17.98        29.16 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BV 
       25.74        19.79        12.85        20.91        26.73         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
        8.25        27.45        18.08         7.10        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK 
       18.81         6.15        12.69         2.27         3.06        10.85 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3IB TCGA-G2-A3IE 
       10.65        17.23        11.08        61.94         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       17.62        66.02         0.49         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
        2.10         2.20        10.92        10.65        32.98         7.00 
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-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB 
       19.40        64.01         9.01        12.16         3.45         2.76 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R 
       27.68        52.73        50.56        35.97        46.98        44.38 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78P 
       16.67        14.24        38.99        17.62        22.68        78.25 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HC 
       69.34       112.83        29.56        17.82         3.85         6.58 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35        79.66        15.98        34.45        14.93 
TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX 
       12.76        28.24         2.24         7.63         2.96         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       56.48        18.15        11.97        13.64        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-A9RM 
       31.20        21.86        28.41        94.29        88.87        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA51 
       20.22         2.89        34.06        19.69        63.02        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA5H 
       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 
       94.88       104.65         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 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM 
       47.80        29.65         2.50        17.42         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39        13.15        26.14        12.16        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       14.89        14.96         8.35         8.25        17.16        16.18 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS 
        9.96        28.70        28.41         8.98         1.94        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       13.97        12.59        12.13        12.16        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-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90        15.12        18.48        29.79         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        46.68         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
      142.78        87.32         4.80         9.67        20.81       163.30 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
       17.98        64.18        53.29        76.60        67.36        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       38.24        52.01        18.81        15.35        13.64        56.15 
TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       20.32        38.83         0.10         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24         4.24        24.66 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
        1.22        14.07        12.95        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SO 
       16.77         4.01        12.62        27.98        60.66         5.52 
TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
       46.78         7.56        27.35        14.96         3.62        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N 
       53.88        11.01        19.33         5.69        58.92         2.70 
TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.28        12.36         4.31         9.67        31.07        12.66 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94         3.25        48.00        15.95        26.93        59.31 
TCGA-G2-A2ES TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       33.01         6.94        70.32        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81        19.13        15.91        14.07        17.75        24.92 
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        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3QH 
       32.78        20.05         5.62         4.73        14.27         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS 
       36.49        27.35         8.58         1.51        38.60        25.02 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       21.24         9.14         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       15.42        16.27        11.80         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       21.07        13.48        12.23         1.84        16.54        12.43 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PE 
       37.05        86.83        76.01         3.02         3.91         6.21 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       51.32        45.04        97.45       125.49         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9ST TCGA-XF-A9SU 
       48.62        64.80         3.22        66.41         4.21         5.98 
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 
       35.84        13.41         3.48        64.08        58.72         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        54.21 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.49              0.10 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           166.03            163.30 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           18.030            16.225 
[1] "0.5 - 166.0 (18.0)" "0.1 - 163.3 (16.2)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         1       43        50       65
  5Q LOSS WILD-TYPE       1       86        90       70
D51V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               43                86
  STAGE III              50                90
  STAGE IV               65                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
  5Q LOSS MUTATED         40  82  23
  5Q LOSS WILD-TYPE       83 113  35
D51V4, multiclass
          clus
vv         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1+T2              40                83
  T3                    82               113
  T4                    23                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
  5Q LOSS MUTATED    74  21  36   7
  5Q LOSS WILD-TYPE 161  26  39   2
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              74               161
  N1              21                26
  N2              36                39
  N3               7                 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    67   7
  5Q LOSS WILD-TYPE 125   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     67    7
  5Q LOSS WILD-TYPE  125    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              67               125
  1               7                 4
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    41 118
  5Q LOSS WILD-TYPE  66 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     41  118
  5Q LOSS WILD-TYPE   66  183
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              41                66
  MALE               118               183
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   143   6
  5Q LOSS WILD-TYPE 221  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    143    6
  5Q LOSS WILD-TYPE  221   13
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO              143               221
  YES               6                13
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, continuous
D51V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       9                        13   130
  5Q LOSS WILD-TYPE    34                         9   197
D51V12, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN              13                 9
  WHITE                                 130               197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     4 144
  5Q LOSS WILD-TYPE   5 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4  144
  5Q LOSS WILD-TYPE    5  225
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             144               225
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    61  39
  6P LOSS WILD-TYPE 168 138
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              100               306 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               39               138 
$`6P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA82 
       24.13       108.95         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        26.14         5.06         8.25        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42C TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CU-A3QU 
       20.48         4.67        28.70        12.79        12.13         5.19 
TCGA-CU-A5W6 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ 
        1.84        16.70        46.68       142.78        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        50.70        36.66 
TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 
       15.02       165.73       166.03        19.00        13.64        13.64 
TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A7PW TCGA-E7-A97Q 
       12.03        15.35        38.83         0.56        13.68         8.09 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BV 
       23.41        29.16        46.78        20.91        15.58         5.36 
TCGA-FD-A62O TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-G2-A3IE 
        7.10        12.36        31.07        17.23        59.31        20.12 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GU-A767 
       70.32        29.36        19.13        14.07         2.10         4.73 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A4AB 
       21.34        19.82        19.40        38.60        64.01         2.76 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R 
       11.70         1.81        52.73        35.97        46.98        44.38 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A8OD 
       13.48        16.67        14.24        38.99        17.62       112.83 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SM TCGA-XF-A9T0 TCGA-XF-A9T3 
       15.35         1.87        48.62        34.45        26.27         2.24 
TCGA-XF-AAMJ TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN5 
       54.90         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        22.36        25.41        21.11        21.86 
TCGA-ZF-A9R9 TCGA-ZF-AA4N TCGA-ZF-AA51 TCGA-ZF-AA53 
       28.41         2.89        56.35        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        94.88       104.65        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        50.04         0.62        41.75        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       15.12        10.22        47.80        29.65         2.50        17.42 
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-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
        8.35        17.16        12.82         9.96        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         8.98         1.94        23.01        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.59        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       11.34        11.34        11.87        18.58        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 
        4.90        15.12        18.48        29.79        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        17.95         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        4.80         8.15         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       163.30        66.05        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       15.68        38.24        52.01        13.58        18.81        15.35 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       56.15        11.18        20.32        43.59        29.72         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70        25.58         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.24         4.24        24.03        24.66         0.92         1.22 
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-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR 
       60.66        24.30        17.98         5.52        25.74        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR 
       12.85         7.56        27.35        14.96         3.62        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-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-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-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        9.67        10.85        12.66        10.65         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
       11.08        61.94        48.00        15.95        26.93        33.01 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 
        7.23        17.62        66.02         6.94        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.81        15.91        17.75        24.92         0.49         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        18.97         7.63        32.78        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX 
        5.62        10.65        32.98         7.00        14.27        19.10 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        36.49        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       22.72         1.51         9.01        12.16        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB 
       21.24         9.14        27.68         9.07        17.72        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        50.56         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78L 
       21.07        12.23         1.84        16.54        12.43        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       22.68        86.83        76.01        78.25        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
        3.91        29.56        17.82         6.21         3.85        51.32 
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-A9SK TCGA-XF-A9SL TCGA-XF-A9SP 
       64.80        79.66         3.22        15.98        66.41        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        4.21         5.98        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       28.24        18.90        16.27        66.64         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-AAMX TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
       91.73         2.96         6.77        98.99        30.94        61.45 
TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        18.15         3.88        18.84         9.63         0.66 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       31.20        30.28        35.84        94.29        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R 
       64.08        58.72        88.87        47.84        20.22        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       19.69         8.61        59.38        60.16        63.02        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        54.21        19.17         5.52        12.23 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.56              0.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           166.03            163.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           20.300            16.205 
[1] "0.6 - 166.0 (20.3)" "0.1 - 163.3 (16.2)"
[1] "hr=" "1.4"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         1       26        33       39
  6P LOSS WILD-TYPE       1      103       107       96
D52V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               26               103
  STAGE III              33               107
  STAGE IV               39                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  6P LOSS MUTATED         23  47  19
  6P LOSS WILD-TYPE      100 148  39
D52V4, multiclass
          clus
vv         6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1+T2              23               100
  T3                    47               148
  T4                    19                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
  6P LOSS MUTATED    51   7  27   3
  6P LOSS WILD-TYPE 184  40  48   6
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              51               184
  N1               7                40
  N2              27                48
  N3               3                 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    56   3
  6P LOSS WILD-TYPE 136   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     56    3
  6P LOSS WILD-TYPE  136    8
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              56               136
  1               3                 8
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    30  70
  6P LOSS WILD-TYPE  77 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     30   70
  6P LOSS WILD-TYPE   77  231
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              30                77
  MALE                70               231
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    91   4
  6P LOSS WILD-TYPE 273  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     91    4
  6P LOSS WILD-TYPE  273   15
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               91               273
  YES               4                15
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, continuous
D52V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       6                         6    81
  6P LOSS WILD-TYPE    37                        16   246
D52V12, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   6                37
  BLACK OR AFRICAN AMERICAN               6                16
  WHITE                                  81               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"
D52V13, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     4  90
  6P LOSS WILD-TYPE   5 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4   90
  6P LOSS WILD-TYPE    5  279
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO              90               279
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    88  71
  6Q LOSS WILD-TYPE 141 106
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              159               247 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               71               106 
$`6Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA7W 
       24.13       108.95         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        26.14 
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-CF-A3MG TCGA-CF-A3MI TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A6 
       12.79        12.13        12.16         5.19         1.84        66.41 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       16.70        46.68        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV 
       13.58        17.72        50.27        21.30        17.98        64.18 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       50.70        36.66        38.24        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 
      166.03        18.81        19.00        13.64        13.64        12.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD 
       43.59        15.35        38.83        22.16         0.56         4.24 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SN 
        1.22        13.68         8.09         8.94        23.41        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU 
       46.78        19.79        20.91        15.58        26.73        19.33 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P 
        5.36         8.25        27.45        18.08         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 
       13.35         6.15        12.36         3.06         4.31        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3B 
       17.23        11.08        59.31        33.01        20.12        66.02 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I1 
       70.32        29.36        20.71        19.13        14.07         8.94 
TCGA-GD-A3OP TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
        2.10        18.97         7.63         4.73        32.98         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A6ZA 
       21.34        19.10        19.82        20.28         8.48        22.72 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-A6FZ 
       19.40        38.60        64.01         2.76        11.70         1.81 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 
       52.73        50.56        35.97        46.98        44.38        15.58 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       13.48        16.67        14.24        12.43        38.99        17.62 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB 
       22.68        69.34       112.83        29.56         3.85        45.04 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       15.35         1.87        48.62         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMJ 
       14.93         4.21        11.90        26.27         2.24        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 
        7.63        91.73         8.32        44.32        56.48        86.30 
TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
       75.39        11.97        13.64        22.36        25.41        21.11 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA51 TCGA-ZF-AA52 
       21.86        28.41         2.89        34.06        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       57.90        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        94.88       104.65        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        50.04         0.62        66.54        15.12        47.80 
TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       29.65         2.50        17.42         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-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.89        14.96         8.35         8.25        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        36.43        28.41         8.98 
TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S 
       23.01        12.56        13.97        12.59        13.08        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-A9FL 
       12.00        12.10        11.34        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
       13.08        12.92         4.90        15.12        18.48        29.79 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC 
       13.58        21.86         2.14        18.41        19.00       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IM 
      112.44        16.14        17.62        15.62        87.32         8.15 
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       163.30 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6M 
       66.05        53.29        76.60        67.36        15.68        52.01 
TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.35        56.15        11.18        20.32        29.72         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70        25.58         0.66        26.96        26.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       24.03        24.66         0.92        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.37        32.02        16.77        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO 
       22.52        27.98        60.66        24.30        17.98         5.52 
TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
       25.74        12.85         7.56        27.35        14.96         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A6TA 
       53.88        11.01         5.69        58.92         2.70        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
       18.81        12.69         2.27         9.67        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.65         8.94         3.25        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO 
       26.93         7.23        17.62         6.94        21.40        15.81 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.91        17.75        24.92         0.49        13.91         7.73 
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-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QI 
       32.78        20.05         5.62        10.65        14.27        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE 
       27.35         8.58        19.07         1.51         9.01        12.16 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
       25.02         3.45        21.24         9.14        27.68         9.07 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R 
       17.72        15.42        16.27        11.80         1.15        15.32 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78N 
       21.07        12.23         1.84        16.54        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        78.25         3.02         3.91        17.82         6.21 
TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI 
       51.32         6.58        97.45       125.49        97.12        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SX 
       64.80        79.66        66.41         5.98        12.76        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        28.24        18.90        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ 
       13.74        92.98        10.82       110.60        11.31        71.57 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 
        2.96         6.77        98.99        30.94        61.45        27.06 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R3 
       18.15         3.88        18.84         9.63         0.66        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       30.28        35.84        94.29        13.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4U 
       58.72        88.87        47.84        20.22        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       59.38        60.16        63.02         8.52        54.21         5.52 
TCGA-ZF-AA5P 
       12.23 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.56              0.10 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           166.03            163.30 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            19.10             15.95 
[1] "0.6 - 166.0 (19.1)" "0.1 - 163.3 (15.9)"
[1] "hr=" "1"  
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         1       43        46       68
  6Q LOSS WILD-TYPE       1       86        94       67
D53V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               43                86
  STAGE III              46                94
  STAGE IV               68                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
  6Q LOSS MUTATED         41  79  25
  6Q LOSS WILD-TYPE       82 116  33
D53V4, multiclass
          clus
vv         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1+T2              41                82
  T3                    79               116
  T4                    25                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
  6Q LOSS MUTATED    76  20  41   5
  6Q LOSS WILD-TYPE 159  27  34   4
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              76               159
  N1              20                27
  N2              41                34
  N3               5                 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    74   3
  6Q LOSS WILD-TYPE 118   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     74    3
  6Q LOSS WILD-TYPE  118    8
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              74               118
  1               3                 8
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    44 115
  6Q LOSS WILD-TYPE  63 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     44  115
  6Q LOSS WILD-TYPE   63  186
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              44                63
  MALE               115               186
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   144   5
  6Q LOSS WILD-TYPE 220  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    144    5
  6Q LOSS WILD-TYPE  220   14
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO              144               220
  YES               5                14
[1] 2 2
[1] FALSE
D53V9, continuous
D53V10, continuous
D53V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       9                        10   130
  6Q LOSS WILD-TYPE    34                        12   197
D53V12, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN              10                12
  WHITE                                 130               197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     6 141
  6Q LOSS WILD-TYPE   3 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      6  141
  6Q LOSS WILD-TYPE    3  228
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 3
  NOT HISPANIC OR LATINO             141               228
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    10  10
  7P LOSS WILD-TYPE 219 167
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               20               386 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               10               167 
$`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        50.70 
TCGA-DK-AA6W TCGA-DK-AA77 TCGA-FD-A5BY TCGA-FD-A6TA TCGA-GU-AATO TCGA-GV-A3QF 
       13.64        20.32         8.25        62.86        10.65        20.28 
TCGA-K4-A3WS TCGA-KQ-A41Q TCGA-XF-AAML TCGA-XF-AAMZ TCGA-ZF-A9RL TCGA-ZF-AA4T 
       25.02        46.98         7.63        44.32        88.87        19.69 
TCGA-ZF-AA54 TCGA-ZF-AA58 
       19.40        54.21 

$`7P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I 
       10.22        47.80        29.65         2.50        17.42         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        26.14 
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        36.43 
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        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90        15.12        18.48         5.19        29.79 
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-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       46.68        17.95         7.79       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         8.15         8.22        17.72        50.27        21.30 
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       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       36.66        38.24        52.01        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        18.81        19.00        15.35        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       11.18        12.03        43.59        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
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         7.56        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-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         5.69        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10         6.28        13.35        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-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07        12.66        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 
       11.08        61.94        48.00        15.95        26.93        59.31 
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 
       70.32        29.36        21.40        20.71        15.81        19.13 
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        18.97         7.63        32.78 
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-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.10        19.82         8.48        36.49        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-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       64.01         9.01        12.16         3.45        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        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
       15.42        16.27        11.80        52.73        50.56        35.97 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       44.38         1.15        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        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       38.99        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 
       78.25        69.34         3.02       112.83         3.91        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC 
       17.82         6.21         3.85        51.32        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-A9SK TCGA-XF-A9SL 
       48.62        64.80        79.66         3.22        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       34.45        14.93         4.21         5.98        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-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
      110.60        11.31        54.90        71.57        91.73         2.96 
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-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H 
       86.30        27.06        75.39        18.15         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        22.36        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        31.20        30.28        35.84        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       94.29        13.41         3.48        64.08        58.72        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-AA56 TCGA-ZF-AA5H 
       63.02        56.35        35.41        57.90         8.52        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             2.14              0.10 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            88.87            166.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             20.3              16.8 
[1] "2.1 - 88.9 (20.3)"  "0.1 - 166.0 (16.8)"
[1] "hr=" "1"  
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED         1        6         5        9
  7P LOSS WILD-TYPE       1      123       135      126
D54V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II                6               123
  STAGE III               5               135
  STAGE IV                9               126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  7P LOSS MUTATED          6   9   5
  7P LOSS WILD-TYPE      117 186  53
D54V4, multiclass
          clus
vv         7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1+T2               6               117
  T3                     9               186
  T4                     5                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
  7P LOSS MUTATED     9   0   8   1
  7P LOSS WILD-TYPE 226  47  67   8
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               9               226
  N1               0                47
  N2               8                67
  N3               1                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     8   0
  7P LOSS WILD-TYPE 184  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8    0
  7P LOSS WILD-TYPE  184   11
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               8               184
  1               0                11
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3  18
  7P LOSS WILD-TYPE 104 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3   18
  7P LOSS WILD-TYPE  104  283
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3               104
  MALE                18               283
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    17   2
  7P LOSS WILD-TYPE 347  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     17    2
  7P LOSS WILD-TYPE  347   17
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               17               347
  YES               2                17
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, continuous
D54V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         1    19
  7P LOSS WILD-TYPE    42                        21   308
D54V12, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                42
  BLACK OR AFRICAN AMERICAN               1                21
  WHITE                                  19               308
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  20
  7P LOSS WILD-TYPE   9 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   20
  7P LOSS WILD-TYPE    9  349
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              20               349
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    16  11
  7Q LOSS WILD-TYPE 213 166
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               27               379 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               11               166 
$`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       142.78         4.80 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-E7-A6ME TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TE 
        8.15        15.02        24.03         8.25        18.08        12.36 
TCGA-GC-A4ZW TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATQ TCGA-K4-A3WS TCGA-KQ-A41Q 
        0.49         5.62        10.65         7.00        25.02        46.98 
TCGA-UY-A8OB TCGA-XF-A9SM TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMZ TCGA-YF-AA3M 
       69.34        34.45         7.63         2.96        44.32        13.64 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-AA4T 
       64.08        88.87        19.69 

$`7Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       15.12        10.22        47.80        29.65         2.50        17.42 
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 
       26.14        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-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         8.98         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
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-A9FL 
       12.00        12.10        11.34        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       13.08        12.92         4.90        15.12        18.48         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       29.79         1.84        13.58        21.86        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-A2I6 TCGA-DK-A3IL 
       15.62        46.68        17.95         7.79        87.32        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       163.30        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T 
       38.24        52.01        13.58       165.73       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       19.00        13.64        15.35        13.64        56.15        11.18 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       12.03        20.32        43.59        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        26.96        26.24         4.24        24.66         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-A43U TCGA-FD-A43X 
       12.85         7.56        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-A5BV 
       15.58        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        5.69        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-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07        12.66 
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        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       48.00        15.95        26.93        59.31        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        70.32        29.36 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40        20.71        15.81        19.13        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-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-A767 TCGA-GU-AATP 
       18.97         7.63        32.78        20.05         4.73        32.98 
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-GV-A6ZA TCGA-H4-A2HO 
       36.49        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       19.40        38.60        64.01         9.01        12.16         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-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       50.56        35.97        44.38         1.15        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 
       16.54        12.43        38.99        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        78.25         3.02       112.83         3.91 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
       29.56        17.82         6.21         3.85        51.32        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-A9SK 
       17.88        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       66.41        14.93         4.21         5.98        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-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW 
      110.60        11.31        54.90        71.57        91.73         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        6.77        98.99        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        18.15         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        22.36        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        35.84        21.86        28.41        94.29        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
        3.48        58.72        47.84        20.22         2.89        34.06 
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        56.35        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        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.49              0.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           142.78            166.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.64             17.42 
[1] "0.5 - 142.8 (13.6)" "0.1 - 166.0 (17.4)"
[1] "hr=" "1"  
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED         1        9         8        9
  7Q LOSS WILD-TYPE       1      120       132      126
D55V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II                9               120
  STAGE III               8               132
  STAGE IV                9               126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  7Q LOSS MUTATED          8  14   3
  7Q LOSS WILD-TYPE      115 181  55
D55V4, multiclass
          clus
vv         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1+T2               8               115
  T3                    14               181
  T4                     3                55
[1] 3 2
[1] TRUE
[1] "dimension of 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    13   1   8   0
  7Q LOSS WILD-TYPE 222  46  67   9
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              13               222
  N1               1                46
  N2               8                67
  N3               0                 9
[1] 4 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 181  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11    0
  7Q LOSS WILD-TYPE  181   11
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              11               181
  1               0                11
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     4  23
  7Q LOSS WILD-TYPE 103 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4   23
  7Q LOSS WILD-TYPE  103  278
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               4               103
  MALE                23               278
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    22   1
  7Q LOSS WILD-TYPE 342  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     22    1
  7Q LOSS WILD-TYPE  342   18
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               22               342
  YES               1                18
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, continuous
D55V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       2                         0    24
  7Q LOSS WILD-TYPE    41                        22   303
D55V12, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   2                41
  BLACK OR AFRICAN AMERICAN               0                22
  WHITE                                  24               303
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2  25
  7Q LOSS WILD-TYPE   7 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2   25
  7Q LOSS WILD-TYPE    7  344
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              25               344
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   109  78
  8P LOSS WILD-TYPE 120  99
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              187               219 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               78                99 
$`8P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7Q 
       24.13        11.97       104.65       108.95         8.35        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A0C8 
       17.16        27.62         0.62        10.22         2.50        40.08 
TCGA-BL-A13J TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F 
        2.66         8.35        16.18         9.96        28.70        28.41 
TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
        8.98        12.56        10.95        11.34        11.34        11.87 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AC 
       12.92        18.48         5.19        21.86        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
      112.44        46.68       142.78        87.32         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6B2 
        8.15         8.22        21.30         9.67        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6W 
       50.70        38.24        52.01        15.02       166.03        13.64 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 
       11.18        12.03        20.32        15.35        38.83        25.58 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
        0.56        26.96         4.24         0.92         1.22        13.68 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 
        8.09        16.77         8.94        33.04         4.01        22.52 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A43N 
       24.30        23.41        17.98         5.52        19.79         7.56 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A5BZ 
       27.35        15.58        26.73        19.33         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD 
       18.08         2.70         6.28        13.35        62.86        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         2.27         4.31        10.85        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D 
       11.08        61.94        15.95        20.12         6.94        70.32 
TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       29.36        19.13        15.91        14.07        17.75        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B 
        0.49        13.91         7.73         2.10         3.12         7.36 
TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP 
       10.92         7.63        20.05         5.62        10.65        32.98 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E 
       21.34        19.10        19.82        20.28         8.48         8.58 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07        19.40         9.01        12.16        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        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-KQ-A41R 
        1.81        15.42        11.80        52.73        46.98        44.38 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-UY-A78K TCGA-UY-A78L 
       15.58        21.07        12.23        14.24        17.62        37.05 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PH TCGA-XF-A8HB 
       69.34       112.83        29.56        17.82        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
        6.58         1.87        79.66         3.22        15.98        34.45 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 
        4.21        12.76        11.90        26.27         2.24        66.64 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW 
      110.60        54.90         7.63        71.57         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R4 
       56.48        61.45        75.39        18.84        22.36        30.28 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       13.41         3.48        88.87        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       59.38        60.16        57.90         8.52        54.21        19.17 
TCGA-ZF-AA5P 
       12.23 

$`8P LOSS WILD-TYPE`
TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       94.88        16.27        44.94        16.83        34.98        50.04 
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        29.65 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42         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        26.14        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-A2LD 
       14.89        14.96         5.06         8.25        17.16        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        12.82        17.56        36.43         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.79        13.97        12.59        12.13        13.08        12.16 
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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       12.00        12.10        18.58        13.08         4.90        15.12 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
       29.79         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        17.95         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       163.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
       66.05        17.98        53.29        76.60        67.36        36.66 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       165.73        18.81        19.00        15.35        13.64 
TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       56.15        43.59        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
       16.70         0.66        26.24        24.03        24.66        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 
       12.95        15.32        14.37        32.02        12.62        27.98 
TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S 
       60.66        29.16        25.74        46.78        12.85        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX 
       20.91         3.62        53.88        11.01         5.36         5.69 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI 
       58.92         7.10        18.81         6.15         3.06         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL 
       12.66        10.65         8.94         3.25        48.00        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM 
       59.31        33.01         7.23        17.62        66.02        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       20.71        15.81         8.94        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI 
       18.97        32.78         4.73         7.00        14.27        36.49 
TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI 
       27.35        22.72         1.51        38.60        64.01        11.70 
TCGA-K4-A83P TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V 
       16.27        50.56        35.97         1.15        15.32        13.48 
TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M 
       16.67         1.84        16.54        12.43        38.99        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PE 
       86.83        76.01        78.25         3.02         3.91         6.21 
TCGA-UY-A9PF TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI 
        3.85        97.45       125.49        97.12        15.35        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        66.41        14.93         5.98        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        18.15         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        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        94.29        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA51 
       58.72        47.84        20.22         2.89        63.02        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA5N 
       35.41        19.40         5.52 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.49              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           166.03            165.73 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            16.77             17.62 
[1] "0.5 - 166.0 (16.8)" "0.1 - 165.7 (17.6)"
[1] "hr=" "1"  
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         1       58        55       74
  8P LOSS WILD-TYPE       1       71        85       61
D56V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               58                71
  STAGE III              55                85
  STAGE IV               74                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
  8P LOSS MUTATED         53  90  28
  8P LOSS WILD-TYPE       70 105  30
D56V4, multiclass
          clus
vv         8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1+T2              53                70
  T3                    90               105
  T4                    28                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
  8P LOSS MUTATED    99  25  42   4
  8P LOSS WILD-TYPE 136  22  33   5
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              99               136
  N1              25                22
  N2              42                33
  N3               4                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    75   6
  8P LOSS WILD-TYPE 117   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     75    6
  8P LOSS WILD-TYPE  117    5
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              75               117
  1               6                 5
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    49 139
  8P LOSS WILD-TYPE  58 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     49  139
  8P LOSS WILD-TYPE   58  162
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              49                58
  MALE               139               162
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   165   7
  8P LOSS WILD-TYPE 199  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    165    7
  8P LOSS WILD-TYPE  199   12
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              165               199
  YES               7                12
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, continuous
D56V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED      13                        13   156
  8P LOSS WILD-TYPE    30                         9   171
D56V12, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                  13                30
  BLACK OR AFRICAN AMERICAN              13                 9
  WHITE                                 156               171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4 173
  8P LOSS WILD-TYPE   5 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4  173
  8P LOSS WILD-TYPE    5  196
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             173               196
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    23  15
  8Q LOSS WILD-TYPE 206 162
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               38               368 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               162 
$`8Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-CF-A1HS 
      108.95         8.35         2.50        40.08         2.66        12.56 
TCGA-CF-A8HX TCGA-DK-A2HX TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A6B5 TCGA-DK-AA76 
       11.34        46.68        13.58         8.15        50.70        12.03 
TCGA-DK-AA77 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A7DV TCGA-FD-A3B7 
       20.32         0.56        26.96         4.24         1.22         4.01 
TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A6TK TCGA-FJ-A3Z7 
       23.41        19.79        19.33        27.45        10.85        31.07 
TCGA-G2-AA3F TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-AATO TCGA-H4-A2HQ TCGA-K4-A3WS 
       29.36        10.92         7.63        10.65        19.40        25.02 
TCGA-K4-A3WU TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-UY-A78L TCGA-XF-A9SM TCGA-XF-A9ST 
        3.45        17.72        15.58        37.05        34.45         4.21 
TCGA-XF-AAMQ TCGA-XF-AAN0 
       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 
       24.13        11.97        94.88       104.65        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        50.04 
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-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       47.80        29.65        17.42         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        26.14        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        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
        1.94        23.01        12.79        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        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-A8HY 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.87        18.58        13.08        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       18.48         5.19        29.79         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        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      142.78        87.32         4.80         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       163.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       66.05        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        36.66        38.24        52.01        15.02        13.58 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
      165.73       166.03        18.81        19.00        13.64        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        56.15        11.18        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       29.72         0.10        22.16         2.24        16.70        25.58 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
        0.66        26.24        24.03        24.66         0.92        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77         8.94        33.04        12.62        22.52        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-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       46.78        12.85         7.56        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV 
        3.62        15.58        26.73        53.88        11.01         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-FJ-A3Z9 
       12.36         2.27         3.06         4.31         9.67        12.66 
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        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       48.00        15.95        26.93        59.31        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM 
       20.12        17.62        66.02         6.94        70.32        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       20.71        15.81        19.13        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-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20         7.36        11.31        18.97 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
       32.78        20.05         5.62         4.73        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-GV-A6ZA TCGA-H4-A2HO 
       36.49        27.35         8.58        19.07        22.72         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB 
       38.60        64.01         9.01        12.16        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
        9.14        27.68         9.07        11.70         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       16.27        11.80        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        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        16.54        12.43        38.99 
TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       17.62        22.68        86.83        76.01        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
        3.02       112.83         3.91        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        3.85        51.32        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-A9SK TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9SU 
       79.66         3.22        15.98        66.41        14.93         5.98 
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-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
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-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        18.15 
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 
       22.36        25.41        21.11        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        94.29        13.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       58.72        88.87        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        56.35 
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        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.56              0.10 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           108.95            166.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           16.650            17.195 
[1] "0.6 - 109.0 (16.6)" "0.1 - 166.0 (17.2)"
[1] "hr=" "1"  
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         1       10        10       17
  8Q LOSS WILD-TYPE       1      119       130      118
D57V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               10               119
  STAGE III              10               130
  STAGE IV               17               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
  8Q LOSS MUTATED          9  13  12
  8Q LOSS WILD-TYPE      114 182  46
D57V4, multiclass
          clus
vv         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1+T2               9               114
  T3                    13               182
  T4                    12                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
  8Q LOSS MUTATED    18   5  10   1
  8Q LOSS WILD-TYPE 217  42  65   8
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              18               217
  N1               5                42
  N2              10                65
  N3               1                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    17   2
  8Q LOSS WILD-TYPE 175   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     17    2
  8Q LOSS WILD-TYPE  175    9
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              17               175
  1               2                 9
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    12  26
  8Q LOSS WILD-TYPE  95 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     12   26
  8Q LOSS WILD-TYPE   95  275
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              12                95
  MALE                26               275
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    33   0
  8Q LOSS WILD-TYPE 331  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     33    0
  8Q LOSS WILD-TYPE  331   19
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               33               331
  YES               0                19
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, continuous
D57V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       4                         3    31
  8Q LOSS WILD-TYPE    39                        19   296
D57V12, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   4                39
  BLACK OR AFRICAN AMERICAN               3                19
  WHITE                                  31               296
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  38
  8Q LOSS WILD-TYPE   9 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   38
  8Q LOSS WILD-TYPE    9  331
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              38               331
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   102  72
  9P LOSS WILD-TYPE 127 105
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              174               232 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               72               105 
$`9P LOSS MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        94.88       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-5N-A9KM TCGA-BL-A0C8 
       16.83        34.98        50.04         0.62        17.42        40.08 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
        6.58        19.04        26.14        17.88        19.50        14.89 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
        8.35        16.18        36.43        23.01        12.79        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47V TCGA-CF-A47X 
       12.59        12.13        13.08        12.16        12.46        12.62 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CU-A0YO 
       13.12        12.00        11.34        11.87        18.58         4.90 
TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA 
       18.48         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         4.80         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        66.05        17.98        64.18 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U 
       15.68        50.70        15.02        13.58       166.03        19.00 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 
       13.64        15.35        13.64        11.18        12.03        20.32 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       43.59        38.83        29.72        25.58         0.56         0.66 
TCGA-E7-A6MD TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 
        4.24         0.92         1.22        13.68         8.09         8.94 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       17.98        29.16        46.78        19.79        12.85         7.56 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 
        3.62        15.58        26.73         5.36        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
       58.92         7.10         6.28        62.86        18.81        12.69 
TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3VY 
        3.06        10.85        11.08        59.31         7.23        17.62 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW 
       66.02        29.36        21.40        14.07        24.92         0.49 
TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 
        8.94         2.20         7.36        11.31         7.63         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QK 
       10.65        32.98         7.00        21.34         8.48        27.35 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU 
       22.72        19.40        38.60        64.01        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO 
       21.24         2.76         9.07        11.70        15.42        11.80 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A8JT 
       50.56        35.97        46.98        44.38         1.15        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 
       12.23        16.67        14.24         1.84        16.54        38.99 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HF TCGA-XF-A8HI 
       69.34       112.83        17.82         6.21        97.12        17.88 
TCGA-XF-A9SK TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-A9T4 TCGA-XF-AAMQ 
       15.98         5.98        12.76        26.27        16.27        71.57 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN7 
       91.73         6.77        98.99        44.32        30.94        18.15 
TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       11.97        25.41        21.11        28.41        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       88.87         8.61        60.16        56.35        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 
       24.13        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        29.65 
TCGA-5N-A9KI TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
        2.50         7.33         2.66         6.74        12.39        13.15 
TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       12.16         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       20.48         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T 
       28.41         8.98         1.94        12.56        10.95        12.66 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        12.26        12.10        11.34        13.08        12.92 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
       15.12         5.19        29.79        66.41        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
      112.44        16.14        46.68        17.95         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       87.32        13.58         8.15        23.21         9.67        20.81 
TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L 
      163.30        53.29        76.60        67.36        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A3Y1 
       52.01       165.73        18.81        56.15        15.35         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       22.16         2.24        16.70        26.96        26.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
       24.66        14.07        12.95        15.32        14.37        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-A3SL TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43P 
       60.66        24.30        23.41         5.52        25.74        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       14.96        20.91        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF 
        8.25         2.70        13.35         6.15        12.36         2.27 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        4.31         9.67        31.07        12.66        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        48.00        15.95        26.93 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO 
       33.01        20.12         6.94        70.32        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       19.13        15.91        17.75        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 
        3.12        20.98        10.92        18.97        32.78        20.05 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
        5.62        14.27        19.10        19.82        20.28        36.49 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC 
        8.58        19.07         1.51         9.01        12.16         9.14 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41N TCGA-LC-A66R 
       27.68        17.72         1.81        16.27        52.73        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       15.58        13.48        12.43        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       86.83        76.01        78.25         3.02         3.91        29.56 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        3.85        51.32        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-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX 
       66.41        34.45        14.93         4.21        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        28.24        18.90         2.24        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-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
        7.63         2.96         8.32        56.48        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-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       13.64        22.36        31.20        30.28        35.84        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        64.08        58.72        47.84        20.22         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-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21        19.17         5.52        12.23 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.49              0.10 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           166.03            165.73 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           16.405            17.735 
[1] "0.5 - 166.0 (16.4)" "0.1 - 165.7 (17.7)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         1       54        68       51
  9P LOSS WILD-TYPE       1       75        72       84
D58V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 1                 1
  STAGE II               54                75
  STAGE III              68                72
  STAGE IV               51                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         53  87  25
  9P LOSS WILD-TYPE       70 108  33
D58V4, multiclass
          clus
vv         9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1+T2              53                70
  T3                    87               108
  T4                    25                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
  9P LOSS MUTATED   110  17  30   4
  9P LOSS WILD-TYPE 125  30  45   5
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             110               125
  N1              17                30
  N2              30                45
  N3               4                 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    85   4
  9P LOSS WILD-TYPE 107   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     85    4
  9P LOSS WILD-TYPE  107    7
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              85               107
  1               4                 7
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    44 131
  9P LOSS WILD-TYPE  63 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     44  131
  9P LOSS WILD-TYPE   63  170
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              44                63
  MALE               131               170
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   157  10
  9P LOSS WILD-TYPE 207   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    157   10
  9P LOSS WILD-TYPE  207    9
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              157               207
  YES              10                 9
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, continuous
D58V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED      19                         8   139
  9P LOSS WILD-TYPE    24                        14   188
D58V12, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                  19                24
  BLACK OR AFRICAN AMERICAN               8                14
  WHITE                                 139               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     4 159
  9P LOSS WILD-TYPE   5 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  159
  9P LOSS WILD-TYPE    5  210
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             159               210
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   101  68
  9Q LOSS WILD-TYPE 128 109
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              169               237 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               68               109 
$`9Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04         0.62        66.54 
TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20P 
       29.65        17.42        40.08         6.58        26.14        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 
       19.50        14.89        16.18        28.70        36.43        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S 
       12.79        13.97        12.59        12.13        13.08        10.95 
TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.46        12.62        13.12        11.34        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       18.58        13.08         4.90        18.48         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG 
       13.58         2.14        19.00       112.44        17.62        15.62 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6AV 
       17.72        50.27        21.30        10.55        17.98        64.18 
TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       50.70        15.02       166.03        19.00        13.64        15.35 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       11.18        12.03        20.32        43.59        38.83        29.72 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A7DU 
       16.70        25.58         0.56         0.66         4.24         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3SM 
        1.22        13.68         8.09         8.94        33.04        17.98 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A43Y 
       46.78        19.79        12.85         7.56         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
       26.73        27.45        18.08        58.92         7.10         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FT-A61P TCGA-G2-A2EK 
       62.86        18.81         2.27         3.06        11.08        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM 
       26.93        59.31        17.62        66.02        29.36        21.40 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
       14.07         0.49         8.94         7.73         2.10         2.20 
TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
       32.78         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF 
       21.34         8.48        19.07        22.72        38.60        64.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-AAQO 
       25.02         3.45        21.24         2.76        11.70        11.80 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FN 
       50.56        35.97        46.98         1.15        21.07        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78O 
       14.24         1.84        16.54        12.43        38.99        76.01 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SK TCGA-XF-A9SU 
      112.83        17.82        97.12        17.88        15.98         5.98 
TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-A9T4 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW 
       12.76        26.27        16.27        71.57        91.73         8.32 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M 
        6.77        44.32        30.94        18.15        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       22.36        25.41        21.11        31.20        28.41        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 
        3.48        88.87        20.22         8.61        60.16        56.35 
TCGA-ZF-AA54 
       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-5N-A9KI TCGA-BL-A13I TCGA-BL-A13J 
       15.12        10.22        47.80         2.50         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R 
        6.74        12.39        13.15        19.04        12.16         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25        17.16        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-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y 
        1.94        12.56        12.16        12.66        12.10        12.26 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A3 
       12.00        12.10        12.92        15.12        29.79        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A2HX 
       66.41        18.41        16.70       130.88        16.14        46.68 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.95         7.79       142.78        87.32         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        8.15         8.22        23.21         9.67        20.81       163.30 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       66.05        53.29        76.60        67.36        15.68        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA71 
       38.24        52.01        13.58       165.73        18.81        13.64 
TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A677 
       56.15        15.35         0.10        22.16         2.24        26.96 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       26.24        24.03        24.66        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37        32.02        16.77         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-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BT 
       25.74        27.35        14.96        20.91        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S 
       19.33         5.36         5.69         8.25         2.70        13.35 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        6.15        12.69        12.36         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        12.66        10.65        17.23         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       61.94        48.00        33.01         7.23        20.12         6.94 
TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
       70.32        20.71        15.81        19.13        15.91        17.75 
TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
       24.92        13.91         3.12        20.98         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JX 
       11.31        18.97         7.63        20.05         5.62        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO 
       19.82        20.28        36.49        27.35         8.58         1.51 
TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
       19.40         9.01        12.16         9.14        27.68         9.07 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        52.73        44.38 
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        78.25        69.34         3.02         3.91 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56         6.21         3.85        51.32        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH 
       97.45       125.49        15.35         1.87        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       79.66         3.22        66.41        34.45        14.93         4.21 
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-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-AAMT TCGA-XF-AAMY TCGA-XF-AAN0 
       11.31        54.90         7.63         2.96        98.99        56.48 
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-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
        9.63         0.66        30.28        35.84        21.86        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       64.08        58.72        47.84         2.89        34.06        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 
       59.38        63.02        35.41        57.90         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        12.23 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.49              0.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           166.03            165.73 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            17.62             17.16 
[1] "0.5 - 166.0 (17.6)" "0.1 - 165.7 (17.2)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         2       57        61       49
  9Q LOSS WILD-TYPE       0       72        79       86
D59V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 2                 0
  STAGE II               57                72
  STAGE III              61                79
  STAGE IV               49                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
  9Q LOSS MUTATED         56  79  24
  9Q LOSS WILD-TYPE       67 116  34
D59V4, multiclass
          clus
vv         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1+T2              56                67
  T3                    79               116
  T4                    24                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
  9Q LOSS MUTATED   105  16  28   4
  9Q LOSS WILD-TYPE 130  31  47   5
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             105               130
  N1              16                31
  N2              28                47
  N3               4                 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    89   4
  9Q LOSS WILD-TYPE 103   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     89    4
  9Q LOSS WILD-TYPE  103    7
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              89               103
  1               4                 7
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    43 127
  9Q LOSS WILD-TYPE  64 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     43  127
  9Q LOSS WILD-TYPE   64  174
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              43                64
  MALE               127               174
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   152  10
  9Q LOSS WILD-TYPE 212   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    152   10
  9Q LOSS WILD-TYPE  212    9
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              152               212
  YES              10                 9
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, continuous
D59V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED      20                         6   134
  9Q LOSS WILD-TYPE    23                        16   193
D59V12, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                  20                23
  BLACK OR AFRICAN AMERICAN               6                16
  WHITE                                 134               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"
D59V13, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     3 152
  9Q LOSS WILD-TYPE   6 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3  152
  9Q LOSS WILD-TYPE    6  217
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             152               217
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    40  34
  10P LOSS WILD-TYPE 189 143
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                74                332 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                34                143 
$`10P LOSS MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA82 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20U 
       11.97       104.65        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        13.97 
TCGA-CF-A8HY TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A2I2 TCGA-DK-A3IS 
       11.34         4.90        15.12        18.48         7.79        50.27 
TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       67.36        38.24        52.01        19.00        13.64        15.35 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B4 
       11.18        12.03        43.59        15.35        25.58        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43Y 
        8.94         4.01        22.52        19.79         7.56        15.58 
TCGA-FD-A5BY TCGA-FD-A6TD TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EL 
        8.25        12.69        31.07        10.65        17.23        26.93 
TCGA-G2-A3IB TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GV-A3JX TCGA-GV-A40G 
        7.23        21.40        15.91        13.91        19.10        19.07 
TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A5RH TCGA-K4-A5RI TCGA-KQ-A41O TCGA-LT-A5Z6 
       19.40         3.45         9.07        11.70        50.56        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A78O TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HE 
       13.48        12.23        76.01        29.56         6.21       125.49 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SV TCGA-XF-AAMF TCGA-XF-AAMJ 
        1.87        48.62        79.66        12.76        10.82        54.90 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-AA4N 
        6.77        11.97        25.41        13.41         3.48         2.89 
TCGA-ZF-AA4W TCGA-ZF-AA4X 
       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 
       24.13        94.88       108.95         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        50.04 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ 
       29.65         2.50        17.42         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        26.14        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50         5.06        14.89         5.06         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
       16.18         4.67        12.82         9.96        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG 
       28.41         8.98        12.79        12.56        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A3YL 
       11.87        18.58        13.08        12.92         5.19        29.79 
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-A2I6 TCGA-DK-A3IK 
       15.62        46.68        17.95       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         8.15         8.22        17.72        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       163.30        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        53.29        76.60        15.68        50.70        36.66 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA71 
       15.02        13.58       165.73       166.03        18.81        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       56.15        20.32        38.83        29.72         0.10        22.16 
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        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
        4.24        24.03        24.66         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-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       33.04        12.62        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-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-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01        19.33         5.36         5.69        27.45        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-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        9.67        10.85        12.66         8.94         3.25        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
       61.94        48.00        15.95        59.31        33.01        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 
       17.62        66.02         6.94        70.32        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       15.81        19.13        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        18.97         7.63        32.78 
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-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        21.34        19.82        20.28         8.48        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF 
       27.35         8.58        22.72         1.51        38.60        64.01 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01        12.16        25.02        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       27.68        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       52.73        35.97        46.98        44.38         1.15        15.32 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       21.07        16.67        14.24         1.84        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P 
       38.99        17.62        37.05        22.68        86.83        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       69.34         3.02       112.83         3.91        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       51.32        45.04         6.58        97.45        97.12        15.35 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
       17.88        64.80         3.22        15.98        66.41        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       14.93         4.21         5.98        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-AAMG TCGA-XF-AAMH TCGA-XF-AAML 
        2.10        13.74        92.98       110.60        11.31         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ 
       71.57        91.73         2.96         8.32        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 
       18.15         3.88        18.84         9.63         0.66        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       22.36        21.11        31.20        30.28        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       28.41        94.29        64.08        58.72        88.87        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA51 
       20.22        34.06        19.69         8.61        59.38        56.35 
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        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.87               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            125.49             166.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             15.58              17.62 
[1] "1.9 - 125.5 (15.6)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.1"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         1       26        24       23
  10P LOSS WILD-TYPE       1      103       116      112
D60V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                26                103
  STAGE III               24                116
  STAGE IV                23                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
  10P LOSS MUTATED         23  30   9
  10P LOSS WILD-TYPE      100 165  49
D60V4, multiclass
          clus
vv         10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1+T2               23                100
  T3                     30                165
  T4                      9                 49
[1] 3 2
[1] TRUE
[1] "dimension of 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    45   8  12   2
  10P LOSS WILD-TYPE 190  39  63   7
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               45                190
  N1                8                 39
  N2               12                 63
  N3                2                  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"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    33   3
  10P LOSS WILD-TYPE 159   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     33    3
  10P LOSS WILD-TYPE  159    8
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               33                159
  1                3                  8
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    20  54
  10P LOSS WILD-TYPE  87 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20   54
  10P LOSS WILD-TYPE   87  247
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               20                 87
  MALE                 54                247
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    66   6
  10P LOSS WILD-TYPE 298  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     66    6
  10P LOSS WILD-TYPE  298   13
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                66                298
  YES                6                 13
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, continuous
D60V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       4                         9    55
  10P LOSS WILD-TYPE    39                        13   272
D60V12, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                9                 13
  WHITE                                   55                272
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  67
  10P LOSS WILD-TYPE   7 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   67
  10P LOSS WILD-TYPE    7  302
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               67                302
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    69  59
  10Q LOSS WILD-TYPE 160 118
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               128                278 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                59                118 
$`10Q LOSS MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-BL-A0C8 TCGA-BL-A13J 
       11.97       104.65        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 
       26.14        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        13.97        11.34         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A2I2 
       15.12        18.48         5.19         2.14        46.68         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3X1 
       87.32         4.80        13.58         8.15        50.27        66.05 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R 
       67.36        36.66        38.24        52.01        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA75 TCGA-DK-AA76 
      166.03        19.00        13.64        15.35        11.18        12.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME 
       43.59        15.35        29.72        22.16        25.58        24.03 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P 
        1.22         4.01        22.52        19.79         7.56        27.35 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-FD-A6TE 
       20.91        15.58         8.25        58.92        12.69        12.36 
TCGA-FD-A6TF TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3IB 
        2.27        31.07        10.65        17.23        11.08         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       20.12        17.62        21.40        15.91        14.07        17.75 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A764 
        0.49        13.91         2.10         7.36        10.92        20.05 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40G TCGA-GV-A6ZA 
       21.34        19.10        20.28         8.48        19.07        22.72 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI 
       19.40        25.02         3.45         9.14         9.07        11.70 
TCGA-K4-A6FZ TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.81        50.56        35.97         1.15        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        69.34         3.91        17.82         6.21 
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-A9SP TCGA-XF-A9SV TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMW 
       14.93        12.76        10.82        54.90         7.63         8.32 
TCGA-XF-AAMX TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE 
        6.77        18.15        11.97        13.64        21.11         3.48 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X 
       20.22         2.89        34.06        19.69         8.61        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 
       56.35        35.41 

$`10Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       24.13        94.88       108.95         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        50.04         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        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
        2.50        17.42         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-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.89         5.06         8.25        16.18         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS 
        9.96        36.43        28.41         8.98        12.79        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        11.34        11.87        18.58        13.08        12.92 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       29.79         1.84        13.58        21.86        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-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
       15.62        17.95       142.78         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       23.21         9.67        20.81        10.55       163.30        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6Q 
       64.18        53.29        76.60        15.68        50.70        13.58 
TCGA-DK-AA6T TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3Y1 
       18.81        13.64        56.15        20.32        38.83         0.10 
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        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.66         0.92        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-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       33.04        12.62        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-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-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O 
        5.36         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-A6TG 
        6.28        13.35        62.86        18.81         6.15         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE 
        4.31         9.67        10.85        12.66         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        48.00        15.95        26.93        59.31        33.01 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       66.02         6.94        70.32        29.36        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
       19.13        24.92         8.94         7.73         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        32.78         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JZ 
        4.73        10.65        32.98         7.00        14.27        19.82 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF 
       36.49        27.35         8.58         1.51        38.60        64.01 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ 
        9.01        12.16        21.24         2.76        27.68        17.72 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-KQ-A41R 
       15.42        16.27        11.80        52.73        46.98        44.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       15.32        21.07        16.67        14.24         1.84        16.54 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        38.99        17.62        37.05        22.68        86.83 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PF TCGA-UY-A9PH 
       78.25         3.02       112.83        29.56         3.85        51.32 
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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW 
       15.98        66.41        34.45         4.21         5.98        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-AAMG 
       16.27        66.64         2.10        13.74        92.98       110.60 
TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAMZ 
       11.31        71.57        91.73         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-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        3.88        18.84         9.63         0.66        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       31.20        30.28        35.84        21.86        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4V 
       13.41        64.08        58.72        88.87        47.84        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       60.16        57.90        19.40         8.52        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.49               0.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            166.03             163.30 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            15.745             17.720 
[1] "0.5 - 166.0 (15.7)" "0.1 - 163.3 (17.7)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         1       45        39       43
  10Q LOSS WILD-TYPE       1       84       101       92
D61V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                45                 84
  STAGE III               39                101
  STAGE IV                43                 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
  10Q LOSS MUTATED         39  57  16
  10Q LOSS WILD-TYPE       84 138  42
D61V4, multiclass
          clus
vv         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1+T2               39                 84
  T3                     57                138
  T4                     16                 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
  10Q LOSS MUTATED    66  13  23   4
  10Q LOSS WILD-TYPE 169  34  52   5
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               66                169
  N1               13                 34
  N2               23                 52
  N3                4                  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    54   5
  10Q LOSS WILD-TYPE 138   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     54    5
  10Q LOSS WILD-TYPE  138    6
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               54                138
  1                5                  6
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    33  95
  10Q LOSS WILD-TYPE  74 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     33   95
  10Q LOSS WILD-TYPE   74  206
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               33                 74
  MALE                 95                206
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   110   9
  10Q LOSS WILD-TYPE 254  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    110    9
  10Q LOSS WILD-TYPE  254   10
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO               110                254
  YES                9                 10
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, continuous
D61V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       8                         8   104
  10Q LOSS WILD-TYPE    35                        14   223
D61V12, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    8                 35
  BLACK OR AFRICAN AMERICAN                8                 14
  WHITE                                  104                223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4 116
  10Q LOSS WILD-TYPE   5 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  116
  10Q LOSS WILD-TYPE    5  253
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO              116                253
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    98  82
  11P LOSS WILD-TYPE 131  95
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               180                226 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                82                 95 
$`11P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 
       24.13       104.65       108.95        16.83        34.98         0.62 
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J 
       15.12        29.65         2.50        17.42        40.08         2.66 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH 
       26.14        14.89         5.06         8.35        17.16         4.67 
TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       17.56        28.70         8.98        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47X 
       13.97        12.59        12.13        13.08        12.16        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        18.48 
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 
       46.68        17.95        87.32         4.80        13.58         8.15 
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-AA75 TCGA-DK-AA76 
       15.02       166.03        19.00        13.64        11.18        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ 
       20.32        43.59        15.35        38.83        29.72        22.16 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW 
       25.58         0.56         4.24        24.03         0.92        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.95        14.37         8.09         8.94        24.30        23.41 
TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BZ 
       29.16        12.85         7.56        15.58        26.73        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
       18.08        58.92         2.70         7.10        13.35        62.86 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
        6.15         2.27         3.06         4.31        31.07        10.65 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F 
       11.08        59.31        33.01        66.02        70.32        29.36 
TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
       21.40        14.07        24.92         7.73         2.10         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
        7.36        11.31        18.97         4.73        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
       14.27        21.34        20.28        19.07        22.72        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO 
       38.60        64.01         9.01        11.70        15.42        11.80 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A8JT 
       52.73        50.56        46.98        44.38         1.15        21.07 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M 
       14.24         1.84        16.54        12.43        38.99        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HG 
       76.01        69.34         3.02        17.82         6.21        15.35 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU 
       48.62        64.80         3.22        14.93         4.21         5.98 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAMJ 
       12.76        11.90        66.64         2.10       110.60        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-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       44.32        56.48        18.15        11.97        22.36        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-A9RM 
       21.11        30.28        94.29        13.41        88.87        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA5H 
       20.22        34.06        19.69         8.61        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        94.88         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        50.04        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 
       36.43        28.41         1.94        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A8HX TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       12.10        12.26        11.34        18.58        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 
        4.90        15.12         5.19        29.79        21.86        18.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       19.00       130.88        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
      142.78         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 
      163.30        66.05        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T 
       50.70        36.66        52.01        13.58       165.73        18.81 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        13.64        56.15         0.10         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.66        26.96        26.24        24.66         1.22        14.07 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       15.32        32.02        16.77        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       22.52        27.98        60.66        17.98         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       46.78        19.79        27.35        14.96        20.91         3.62 
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-A62P TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FD-A6TK 
        6.28        18.81        12.69        12.36         9.67        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        17.23         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       15.95        26.93         7.23        20.12        17.62         6.94 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A4ZW 
       20.71        15.81        19.13        15.91        17.75         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A762 
        8.94        13.91         3.12        20.98        10.92         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.78        20.05         5.62        10.65        19.10        19.82 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A5NE 
        8.48        36.49        27.35         8.58         1.51        12.16 
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-A83P TCGA-KQ-A41P TCGA-LC-A66R 
        9.07        17.72         1.81        16.27        35.97        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78L 
       15.58        13.48        12.23        16.67        17.62        37.05 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF 
       86.83        78.25       112.83         3.91        29.56         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       51.32        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
        1.87        17.88        79.66        15.98        66.41        34.45 
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-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMY 
       16.27        13.74        92.98        10.82        11.31        98.99 
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-A9R3 TCGA-ZF-A9R5 
       18.84         9.63         0.66        13.64        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N 
       21.86        28.41         3.48        64.08        58.72         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       59.38        60.16        56.35        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21         5.52        12.23 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.56               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            166.03             165.73 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            16.995             17.425 
[1] "0.6 - 166.0 (17.0)" "0.1 - 165.7 (17.4)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         1       52        55       72
  11P LOSS WILD-TYPE       1       77        85       63
D62V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                52                 77
  STAGE III               55                 85
  STAGE IV                72                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  11P LOSS MUTATED         57  89  28
  11P LOSS WILD-TYPE       66 106  30
D62V4, multiclass
          clus
vv         11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1+T2               57                 66
  T3                     89                106
  T4                     28                 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
  11P LOSS MUTATED    95  25  42   3
  11P LOSS WILD-TYPE 140  22  33   6
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               95                140
  N1               25                 22
  N2               42                 33
  N3                3                  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"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    90   7
  11P LOSS WILD-TYPE 102   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     90    7
  11P LOSS WILD-TYPE  102    4
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               90                102
  1                7                  4
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    48 133
  11P LOSS WILD-TYPE  59 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     48  133
  11P LOSS WILD-TYPE   59  168
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               48                 59
  MALE                133                168
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   158  10
  11P LOSS WILD-TYPE 206   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    158   10
  11P LOSS WILD-TYPE  206    9
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO               158                206
  YES               10                  9
[1] 2 2
[1] FALSE
D62V9, continuous
D62V10, continuous
D62V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED      25                         9   136
  11P LOSS WILD-TYPE    18                        13   191
D62V12, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                   25                 18
  BLACK OR AFRICAN AMERICAN                9                 13
  WHITE                                  136                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5 160
  11P LOSS WILD-TYPE   4 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5  160
  11P LOSS WILD-TYPE    4  209
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO              160                209
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    71  60
  11Q LOSS WILD-TYPE 158 117
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               131                275 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                60                117 
$`11Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA89 
       24.13       104.65       108.95        16.83        34.98        29.65 
TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V 
        2.50        40.08         2.66        26.14        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        17.16         4.67        17.56        28.70         8.98 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X 
       12.56        13.97        12.59        12.13        12.16        12.62 
TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 
       13.12        12.10        11.34        18.48         1.84         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IL 
       66.41        16.70       112.44        17.95        87.32        13.58 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6P 
        8.22        17.72        50.27        64.18        36.66        15.02 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ 
      166.03        13.64        11.18        43.59        15.35        22.16 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW 
       25.58         0.56         4.24        24.03         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         7.56 
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        11.08        59.31 
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        64.01         9.01 
TCGA-K4-A5RI TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-SY-A9G5 
       11.70        50.56        46.98        44.38         1.15        38.99 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HG 
       76.01        69.34       112.83        29.56         6.21        15.35 
TCGA-XF-A9SG TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       48.62        34.45        14.93         5.98        12.76        11.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMT 
       66.64         2.10       110.60        54.90        71.57         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-A9R0 TCGA-ZF-A9R2 
        8.32        56.48        61.45        18.15        22.36        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29        13.41        20.22        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
        8.61        63.02        19.40        54.21        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        94.88         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        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A13I 
       66.54        15.12        10.22        47.80        17.42         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-A20X TCGA-BT-A2LB 
       17.88        19.50         5.06        14.96         8.25        16.18 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       20.48        12.82         9.96        36.43        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01        12.79        13.08        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FL 
       12.10        12.26        12.00        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08        12.92         4.90        15.12         5.19        29.79 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE 
       13.58        21.86        18.41        19.00       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        46.68         7.79       142.78         4.80 
TCGA-DK-A3IM TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        8.15        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 
      163.30        66.05        17.98        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R 
       15.68        50.70        38.24        52.01        13.58       165.73 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       18.81        19.00        15.35        13.64        56.15        12.03 
TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       20.32        38.83        29.72         0.10         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
        0.66        26.96        26.24        24.66         1.22        14.07 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       15.32        32.02        16.77        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-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
        5.52        25.74        46.78        19.79        12.85        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
       19.33         5.69        27.45         6.28        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
       12.69        12.36         2.27         3.06         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07        12.66        10.65        17.23         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        48.00        15.95        26.93         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 
       17.62        66.02         6.94        70.32        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW 
       15.81        19.13        15.91        14.07        17.75         0.49 
TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 
       13.91         3.12        20.98        10.92        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       32.78        20.05         5.62         4.73        10.65        32.98 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E 
       19.10        19.82        20.28         8.48        36.49         8.58 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       22.72         1.51        12.16        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        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41P TCGA-LC-A66R 
       15.42        16.27        11.80        52.73        35.97        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-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84        16.54        12.43        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       86.83        78.25         3.02         3.91        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       51.32        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.87        17.88        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9ST TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       66.41         4.21        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        16.27        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       11.31         7.63        91.73         6.77        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       30.94        86.30        27.06        75.39         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        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41         3.48        64.08        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
       88.87        47.84         2.89        59.38        60.16        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        57.90         8.52         5.52        12.23 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.56               0.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            166.03             165.73 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             16.83              17.42 
[1] "0.6 - 166.0 (16.8)" "0.1 - 165.7 (17.4)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         1       37        46       46
  11Q LOSS WILD-TYPE       1       92        94       89
D63V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                37                 92
  STAGE III               46                 94
  STAGE IV                46                 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
  11Q LOSS MUTATED         42  63  22
  11Q LOSS WILD-TYPE       81 132  36
D63V4, multiclass
          clus
vv         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1+T2               42                 81
  T3                     63                132
  T4                     22                 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
  11Q LOSS MUTATED    71  18  25   1
  11Q LOSS WILD-TYPE 164  29  50   8
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               71                164
  N1               18                 29
  N2               25                 50
  N3                1                  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"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    64   3
  11Q LOSS WILD-TYPE 128   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     64    3
  11Q LOSS WILD-TYPE  128    8
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               64                128
  1                3                  8
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    40  91
  11Q LOSS WILD-TYPE  67 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     40   91
  11Q LOSS WILD-TYPE   67  210
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               40                 67
  MALE                 91                210
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   114   9
  11Q LOSS WILD-TYPE 250  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    114    9
  11Q LOSS WILD-TYPE  250   10
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               114                250
  YES                9                 10
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, continuous
D63V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED      18                         7    98
  11Q LOSS WILD-TYPE    25                        15   229
D63V12, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                   18                 25
  BLACK OR AFRICAN AMERICAN                7                 15
  WHITE                                   98                229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3 115
  11Q LOSS WILD-TYPE   6 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3  115
  11Q LOSS WILD-TYPE    6  254
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              115                254
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    29  27
  12P LOSS WILD-TYPE 200 150
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                56                350 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                27                150 
$`12P LOSS MUTATED`
TCGA-2F-A9KW TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A2LA TCGA-C4-A0F0 
        8.35         2.50        40.08         2.66        17.16         1.94 
TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A3IV 
       12.16        12.62         5.19         1.84       130.88         9.67 
TCGA-E5-A2PC TCGA-E7-A97Q TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       43.59         8.09        23.41        46.78        19.79         7.56 
TCGA-FD-A43X TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-FD-A6TH TCGA-G2-AA3D TCGA-G2-AA3F 
        3.62        18.08        12.36         4.31        70.32        29.36 
TCGA-GC-A3YS TCGA-GD-A76B TCGA-GV-A3JW TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       24.92         7.36        21.34        44.38         1.15        15.32 
TCGA-PQ-A6FN TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PH 
       16.67        12.43        22.68       112.83        17.82        51.32 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SP 
       97.12        15.35         1.87        64.80         3.22        14.93 
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        22.36        64.08        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 
       24.13        11.97        94.88       104.65       108.95        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 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM 
       10.22        47.80        29.65        17.42         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        26.14        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-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35         8.25        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        36.43        28.41         8.98 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       13.08        10.95        12.66        12.46        12.10        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       18.58        13.08        12.92         4.90        15.12        18.48 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
       29.79        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       46.68        17.95         7.79       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         8.15         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21        20.81        10.55       163.30        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        53.29        76.60        67.36        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       36.66        38.24        52.01        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        18.81        19.00        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       56.15        11.18        12.03        20.32        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       29.72         0.10        22.16         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       24.66         0.92         1.22        13.68        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-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16         5.52        25.74        12.85        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91        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-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-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
        6.15        12.69         2.27         3.06         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07        12.66        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 
       11.08        61.94        48.00        15.95        26.93        59.31 
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-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40        20.71        15.81        19.13        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75         0.49         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12        20.98         2.20        10.92        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        32.78        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98         7.00        14.27        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        36.49        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        64.01         9.01        12.16 
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        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-LT-A5Z6 
       11.80        52.73        50.56        35.97        46.98        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        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       38.99        17.62        37.05        86.83        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34         3.02         3.91        29.56         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SG 
       45.04         6.58        97.45       125.49        17.88        48.62 
TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SU 
       79.66        15.98        66.41        34.45         4.21         5.98 
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-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX 
       11.31         7.63        71.57        91.73         2.96         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       98.99        44.32        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        18.15         3.88        18.84         9.63         0.66 
TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       13.64        25.41        21.11        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG 
       21.86        28.41        94.29        13.41         3.48        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4X 
       88.87        47.84         2.89        34.06        59.38        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        57.90        19.40         8.52        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1.15               0.10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            130.88             166.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            16.915             17.325 
[1] "1.1 - 130.9 (16.9)" "0.1 - 166.0 (17.3)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         1       13        19       23
  12P LOSS WILD-TYPE       1      116       121      112
D64V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                13                116
  STAGE III               19                121
  STAGE IV                23                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
  12P LOSS MUTATED         17  24  14
  12P LOSS WILD-TYPE      106 171  44
D64V4, multiclass
          clus
vv         12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1+T2               17                106
  T3                     24                171
  T4                     14                 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
  12P LOSS MUTATED    24   5  16   1
  12P LOSS WILD-TYPE 211  42  59   8
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               24                211
  N1                5                 42
  N2               16                 59
  N3                1                  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"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    21   1
  12P LOSS WILD-TYPE 171  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     21    1
  12P LOSS WILD-TYPE  171   10
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               21                171
  1                1                 10
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    16  40
  12P LOSS WILD-TYPE  91 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     16   40
  12P LOSS WILD-TYPE   91  261
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               16                 91
  MALE                 40                261
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    49   3
  12P LOSS WILD-TYPE 315  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     49    3
  12P LOSS WILD-TYPE  315   16
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                49                315
  YES                3                 16
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, continuous
D64V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       5                         1    48
  12P LOSS WILD-TYPE    38                        21   279
D64V12, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                1                 21
  WHITE                                   48                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"
D64V13, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2  51
  12P LOSS WILD-TYPE   7 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   51
  12P LOSS WILD-TYPE    7  318
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               51                318
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    34  26
  12Q LOSS WILD-TYPE 195 151
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                60                346 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                26                151 
$`12Q LOSS MUTATED`
TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A2LD TCGA-C4-A0F0 
       10.22         2.50        40.08         2.66        20.48         1.94 
TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A2I6 TCGA-DK-A3IV TCGA-DK-AA6R 
       12.16        12.62         5.19        87.32         9.67       165.73 
TCGA-E5-A2PC TCGA-E7-A97Q TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS 
       43.59         8.09        23.41         5.52        46.78        12.85 
TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-AA3D 
        7.56         3.62        12.36         4.31        11.08        70.32 
TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A76B TCGA-GV-A3JW 
       29.36        14.07        24.92         0.49         7.36        21.34 
TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       12.16         9.14        17.72        44.38         1.15        15.32 
TCGA-PQ-A6FN TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PH 
       16.67        12.43        22.68       112.83        17.82        51.32 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9T3 
       97.12        15.35        64.80         3.22        14.93         2.24 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-ZF-A9R0 
       10.82       110.60        54.90         8.32        56.48        22.36 
TCGA-ZF-A9RF TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
       64.08         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 
       24.13        11.97        94.88       104.65       108.95         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        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM 
       15.12        47.80        29.65        17.42         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        26.14        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-A3PH TCGA-BT-A3PJ 
        8.35         8.25        17.16        16.18         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        36.43        28.41         8.98 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       13.08        10.95        12.66        12.46        12.10        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       18.58        13.08        12.92         4.90        15.12        18.48 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       29.79         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        46.68        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        4.80        13.58         8.15         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       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q 
       50.70        36.66        38.24        52.01        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        18.81        19.00        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       56.15        11.18        12.03        20.32        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       29.72         0.10        22.16         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       24.66         0.92         1.22        13.68        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-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S 
       17.98        29.16        25.74        19.79        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       20.91        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-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-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
        6.15        12.69         2.27         3.06         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07        12.66        10.65        17.23         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        48.00        15.95        26.93        59.31        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-A3WC TCGA-GC-A6I1 
       20.71        15.81        19.13        15.91        17.75         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        18.97         7.63        32.78        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        36.49        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-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       64.01         9.01        25.02         3.45        21.24         2.76 
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        16.27 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-LT-A5Z6 
       11.80        52.73        50.56        35.97        46.98        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        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       38.99        17.62        37.05        86.83        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34         3.02         3.91        29.56         6.21         3.85 
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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST 
       48.62        79.66        15.98        66.41        34.45         4.21 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        5.98        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        18.15         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        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        35.84        21.86        28.41        94.29        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        58.72        88.87        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 
       34.06        19.69        59.38        56.35        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21         5.52        12.23 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.49               0.10 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            165.73             166.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            15.335             17.490 
[1] "0.5 - 165.7 (15.3)" "0.1 - 166.0 (17.5)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED         1       15        17       27
  12Q LOSS WILD-TYPE       1      114       123      108
D65V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                15                114
  STAGE III               17                123
  STAGE IV                27                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
  12Q LOSS MUTATED         20  26  13
  12Q LOSS WILD-TYPE      103 169  45
D65V4, multiclass
          clus
vv         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1+T2               20                103
  T3                     26                169
  T4                     13                 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
  12Q LOSS MUTATED    24  10  14   2
  12Q LOSS WILD-TYPE 211  37  61   7
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               24                211
  N1               10                 37
  N2               14                 61
  N3                2                  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"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    25   1
  12Q LOSS WILD-TYPE 167  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     25    1
  12Q LOSS WILD-TYPE  167   10
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               25                167
  1                1                 10
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    15  45
  12Q LOSS WILD-TYPE  92 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     15   45
  12Q LOSS WILD-TYPE   92  256
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               15                 92
  MALE                 45                256
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    50   5
  12Q LOSS WILD-TYPE 314  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     50    5
  12Q LOSS WILD-TYPE  314   14
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                50                314
  YES                5                 14
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, continuous
D65V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       5                         2    51
  12Q LOSS WILD-TYPE    38                        20   276
D65V12, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                2                 20
  WHITE                                   51                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"
D65V13, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  55
  12Q LOSS WILD-TYPE   8 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   55
  12Q LOSS WILD-TYPE    8  314
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               55                314
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    46  40
  13Q LOSS WILD-TYPE 183 137
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                86                320 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                137 
$`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        26.14        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        36.43         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         8.15 
TCGA-DK-A3IN TCGA-DK-A6B6 TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E7-A3X6 TCGA-E7-A4IJ 
        8.22        36.66        13.64        11.18        29.72        22.16 
TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A7DV TCGA-E7-A85H TCGA-FD-A3B5 TCGA-FD-A3B7 
        0.56         4.24         1.22        12.95         8.94         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A43P TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62N 
       24.30        29.16        27.35         5.36        58.92         2.70 
TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3YS 
       17.23        59.31        33.01        29.36        21.40        24.92 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JW TCGA-GV-A3QI 
        8.94        13.91         2.20        11.31        21.34        36.49 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-KQ-A41Q 
       38.60         9.01        21.24         9.14         1.81        46.98 
TCGA-KQ-A41S TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
        1.15        86.83        69.34        29.56        17.82         3.85 
TCGA-XF-A9SM TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMX 
       34.45        21.04        66.64       110.60        54.90         6.77 
TCGA-XF-AAMZ TCGA-ZF-A9R2 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       44.32        21.11        28.41         3.48        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 
       47.84        20.22         2.89        60.16        56.35        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA58 
       19.40        54.21 

$`13Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI 
       41.75        66.54        10.22        47.80        29.65         2.50 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42         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-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F 
        8.35        16.18        20.48        12.82         9.96        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        8.98        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       11.34        11.34        11.87        18.58        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
        4.90        15.12        18.48         5.19        29.79        13.58 
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-A2I4 TCGA-DK-A3IK 
       17.62        15.62        46.68        17.95       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       13.58        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       163.30        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       53.29        76.60        67.36        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T 
       52.01        15.02        13.58       165.73       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       19.00        15.35        13.64        56.15        12.03        20.32 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       43.59        15.35        38.83         0.10         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
       25.58         0.66        26.96        26.24        24.03        24.66 
TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
        0.92        13.68        14.07        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77        33.04        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       60.66        23.41        17.98         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         7.56        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-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        8.25        27.45        18.08         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        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        11.08        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       15.95        26.93         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        6.94        70.32        20.71        15.81        19.13        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        17.75         0.49         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98         7.36        10.92        18.97         7.63        32.78 
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-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
       14.27        19.10        19.82        20.28         8.48        27.35 
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        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH 
       12.16        25.02         3.45         2.76        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       11.70        17.72        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       50.56        35.97        44.38        15.32        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        16.54 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       12.43        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PH 
       78.25         3.02       112.83         3.91         6.21        51.32 
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-A9SK TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       15.98        66.41        14.93         4.21         5.98        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 
       18.15         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        22.36        25.41        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       21.86        94.29        13.41        88.87        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        12.23 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.56               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            130.88             166.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            21.075             16.405 
[1] "0.6 - 130.9 (21.1)" "0.1 - 166.0 (16.4)"
[1] "hr=" "1"  
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         1       23        33       28
  13Q LOSS WILD-TYPE       1      106       107      107
D66V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                23                106
  STAGE III               33                107
  STAGE IV                28                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
  13Q LOSS MUTATED         25  46  10
  13Q LOSS WILD-TYPE       98 149  48
D66V4, multiclass
          clus
vv         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1+T2               25                 98
  T3                     46                149
  T4                     10                 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
  13Q LOSS MUTATED    44  13  13   2
  13Q LOSS WILD-TYPE 191  34  62   7
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               44                191
  N1               13                 34
  N2               13                 62
  N3                2                  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"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    41   1
  13Q LOSS WILD-TYPE 151  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     41    1
  13Q LOSS WILD-TYPE  151   10
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               41                151
  1                1                 10
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    19  67
  13Q LOSS WILD-TYPE  88 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     19   67
  13Q LOSS WILD-TYPE   88  234
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               19                 88
  MALE                 67                234
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    75   5
  13Q LOSS WILD-TYPE 289  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     75    5
  13Q LOSS WILD-TYPE  289   14
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                75                289
  YES                5                 14
[1] 2 2
[1] FALSE
D66V9, continuous
D66V10, continuous
D66V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       5                         8    69
  13Q LOSS WILD-TYPE    38                        14   258
D66V12, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                8                 14
  WHITE                                   69                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"
D66V13, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4  71
  13Q LOSS WILD-TYPE   5 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4   71
  13Q LOSS WILD-TYPE    5  298
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO               71                298
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    73  49
  14Q LOSS WILD-TYPE 156 128
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               122                284 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                49                128 
$`14Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97       104.65       108.95         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-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20V 
        2.50        40.08         2.66        19.04        14.89         5.06 
TCGA-BT-A2LB TCGA-BT-A3PK TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MI TCGA-CF-A47X 
       16.18         9.96        12.79        12.56        12.16        12.62 
TCGA-CF-A5U8 TCGA-CF-A8HY TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 
       13.12        11.34         4.90        15.12         1.84        21.86 
TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IQ 
        2.14       130.88       112.44        17.95        87.32        17.72 
TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-DK-AA6U 
       50.27        66.05        64.18        50.70       166.03        19.00 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DU 
       15.35        38.83        22.16         4.24        24.03         0.92 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5C0 
       29.16        25.74        46.78         7.56        20.91        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH 
       58.92         6.28        62.86         6.15         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-A3VY 
       31.07        17.23        11.08        61.94        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A76B 
       66.02        70.32        19.13        14.07         0.49         7.36 
TCGA-GU-A42Q TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G 
       11.31        32.98        19.82        20.28         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A6MB 
       22.72        19.40        38.60        64.01         3.45        15.42 
TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
       35.97        44.38         1.15        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        38.99        17.62        37.05        22.68        69.34 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HH TCGA-XF-A9SG 
       17.82         6.21         3.85        51.32         1.87        48.62 
TCGA-XF-A9ST TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-AAMJ TCGA-XF-AAML 
        4.21        23.64        28.24        26.27        54.90         7.63 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
        6.77        98.99        44.32        56.48        61.45        86.30 
TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       13.64        94.29        47.84        20.22         2.89        19.69 
TCGA-ZF-AA51 TCGA-ZF-AA52 
       56.35        35.41 

$`14Q LOSS WILD-TYPE`
TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       94.88        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A13I 
       50.04        66.54        10.22        29.65        17.42         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
        6.74        12.39         6.58        13.15        26.14        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         8.35         8.25 
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-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C 
       36.43        28.41         8.98         1.94        23.01        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.59        12.13        13.08        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.10        12.26        12.00        12.10        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       18.58        13.08        12.92        18.48         5.19        29.79 
TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
       13.58        66.41        18.41        19.00        16.70        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        46.68         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       13.58         8.15         8.22        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       163.30        17.98        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       67.36        15.68        36.66        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       165.73        18.81        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 
       56.15        11.18        12.03        20.32        43.59        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10         2.24        16.70        25.58         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       26.96        26.24        24.66         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-A3SO TCGA-FD-A3SR 
       60.66        24.30        23.41        17.98         5.52        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       12.85        27.35        14.96         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-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD 
       27.45         2.70         7.10        13.35        18.81        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.36         2.27         9.67        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94         3.25        48.00        15.95        26.93        59.31 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       33.01         7.23         6.94        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.81        15.91        17.75        24.92         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-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       18.97         7.63        32.78        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       10.65         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       36.49        27.35         1.51         9.01        12.16        25.02 
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-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
       17.72         1.81        16.27        11.80        52.73        50.56 
TCGA-KQ-A41Q TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
       46.98        15.32        15.58        21.07        13.48        16.67 
TCGA-S5-AA26 TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD 
       16.54        86.83        76.01        78.25         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        3.91        29.56        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
       97.12        15.35        17.88        64.80        79.66         3.22 
TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV 
       15.98        66.41        34.45        14.93         5.98        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       11.90        21.04        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-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 
       71.57        91.73         2.96         8.32        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.15         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       11.97        22.36        25.41        21.11        31.20        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       35.84        21.86        28.41        13.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       58.72        88.87        34.06         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       63.02        57.90        19.40         8.52        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.49               0.10 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            166.03             165.73 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            19.100             16.205 
[1] "0.5 - 166.0 (19.1)" "0.1 - 165.7 (16.2)"
[1] "hr=" "1.3"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED         1       36        39       45
  14Q LOSS WILD-TYPE       1       93       101       90
D67V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                36                 93
  STAGE III               39                101
  STAGE IV                45                 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
  14Q LOSS MUTATED         38  55  19
  14Q LOSS WILD-TYPE       85 140  39
D67V4, multiclass
          clus
vv         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1+T2               38                 85
  T3                     55                140
  T4                     19                 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
  14Q LOSS MUTATED    62   9  34   2
  14Q LOSS WILD-TYPE 173  38  41   7
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               62                173
  N1                9                 38
  N2               34                 41
  N3                2                  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    57   3
  14Q LOSS WILD-TYPE 135   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     57    3
  14Q LOSS WILD-TYPE  135    8
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               57                135
  1                3                  8
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    25  97
  14Q LOSS WILD-TYPE  82 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     25   97
  14Q LOSS WILD-TYPE   82  204
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               25                 82
  MALE                 97                204
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   113   3
  14Q LOSS WILD-TYPE 251  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    113    3
  14Q LOSS WILD-TYPE  251   16
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               113                251
  YES                3                 16
[1] 2 2
[1] FALSE
D67V9, continuous
D67V10, continuous
D67V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED      12                         5    99
  14Q LOSS WILD-TYPE    31                        17   228
D67V12, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                   12                 31
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                   99                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"
D67V13, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     4 105
  14Q LOSS WILD-TYPE   5 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4  105
  14Q LOSS WILD-TYPE    5  264
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO              105                264
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    86  59
  15Q LOSS WILD-TYPE 143 118
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               145                261 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                59                118 
$`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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J 
        2.50        17.42        40.08         2.66         6.58        19.04 
TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42B 
       26.14         8.35         8.25        16.18        20.48        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47X 
       28.70        36.43         8.98         1.94        12.56        12.62 
TCGA-CU-A3KJ TCGA-DK-A1A7 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM 
       18.48        18.41         7.79       142.78        87.32         8.15 
TCGA-DK-A3IN TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R 
        8.22        15.68        50.70        52.01        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC 
      166.03        13.64        56.15        11.18        12.03        43.59 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A7DV TCGA-E7-A7PW TCGA-FD-A3B3 TCGA-FD-A3NA 
       22.16        25.58         1.22        13.68        32.02        60.66 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       29.16        25.74         7.56         5.36         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TH 
       18.08        58.92         2.70        13.35        12.69         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL 
       10.85        31.07        17.23        11.08        61.94        26.93 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A4ZW 
       20.12        66.02        15.81        19.13        24.92         0.49 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 
        8.94         2.10         2.20         7.36        10.92         7.63 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E 
        5.62        10.65        19.10        20.28         8.48         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.07        22.72        19.40        38.60        12.16        25.02 
TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-KQ-A41P TCGA-KQ-A41R 
        2.76         9.07        11.70        17.72        35.97        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 
       15.32        15.58        13.48        16.67        14.24        12.43 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       37.05        22.68        76.01         3.91        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.21         3.85        97.45        97.12        15.35         1.87 
TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SU 
       48.62         3.22        15.98        34.45        14.93         5.98 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMG 
       11.90        23.64        26.27         2.24        66.64       110.60 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-YF-AA3L 
        7.63         2.96         6.77        98.99        61.45        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN 
       13.64        30.28        28.41        58.72        88.87        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA58 
        2.89        19.69        63.02        56.35        35.41        54.21 
TCGA-ZF-AA5H 
       19.17 

$`15Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65       108.95        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        50.04        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        29.65         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-A3MF 
        9.96        28.41        23.01        12.79        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.87        18.58        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       15.12         5.19        29.79         1.84        13.58        21.86 
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-A2I1 TCGA-DK-A3IK 
       16.14        17.62        15.62        46.68        17.95         4.80 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       13.58        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       163.30        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q 
       53.29        76.60        67.36        36.66        38.24        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E5-A4TZ 
       18.81        19.00        15.35        13.64        20.32        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        29.72         0.10         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
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        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        3.25        48.00        15.95        59.31        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        70.32        29.36        21.40        20.71 
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        18.97        32.78        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        36.49 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A3WV 
       27.35         1.51        64.01         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        16.27        11.80 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI 
       52.73        50.56        46.98         1.15        21.07        12.23 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78N TCGA-UY-A78P 
        1.84        16.54        38.99        17.62        86.83        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC 
       69.34         3.02       112.83        51.32        45.04         6.58 
TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9ST 
      125.49        17.88        64.80        79.66        66.41         4.21 
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        18.15         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        22.36        25.41        21.11        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RM 
       21.86        94.29        13.41         3.48        64.08        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        12.23 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.49               0.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            166.03             163.30 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             17.23              17.16 
[1] "0.5 - 166.0 (17.2)" "0.1 - 163.3 (17.2)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         1       40        56       47
  15Q LOSS WILD-TYPE       1       89        84       88
D68V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                40                 89
  STAGE III               56                 84
  STAGE IV                47                 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
  15Q LOSS MUTATED         36  77  18
  15Q LOSS WILD-TYPE       87 118  40
D68V4, multiclass
          clus
vv         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1+T2               36                 87
  T3                     77                118
  T4                     18                 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
  15Q LOSS MUTATED    81  16  28   3
  15Q LOSS WILD-TYPE 154  31  47   6
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               81                154
  N1               16                 31
  N2               28                 47
  N3                3                  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    53   4
  15Q LOSS WILD-TYPE 139   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     53    4
  15Q LOSS WILD-TYPE  139    7
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               53                139
  1                4                  7
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    42 103
  15Q LOSS WILD-TYPE  65 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     42  103
  15Q LOSS WILD-TYPE   65  198
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               42                 65
  MALE                103                198
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   132   4
  15Q LOSS WILD-TYPE 232  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    132    4
  15Q LOSS WILD-TYPE  232   15
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               132                232
  YES                4                 15
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, continuous
D68V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       6                         4   127
  15Q LOSS WILD-TYPE    37                        18   200
D68V12, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    6                 37
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                  127                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"
D68V13, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     5 130
  15Q LOSS WILD-TYPE   4 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5  130
  15Q LOSS WILD-TYPE    4  239
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO              130                239
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    64  43
  16P LOSS WILD-TYPE 165 134
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               107                299 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                43                134 
$`16P LOSS MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BL-A0C8 
       24.13        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        26.14         5.06        12.82        36.43        12.56 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AC 
       12.92        18.48         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 
       46.68       142.78        87.32        10.55        17.98        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA76 TCGA-E7-A541 
       36.66        52.01        15.02       165.73        12.03        25.58 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43Y 
       32.02        33.04         5.52        25.74         7.56        15.58 
TCGA-FD-A5BR TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TD 
       26.73        27.45         2.70         7.10        13.35        12.69 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A3IE TCGA-GC-A3RC 
       12.36         4.31        31.07        61.94        20.12        15.91 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
       14.07        24.92         8.94         7.73         2.10         2.20 
TCGA-GU-A42P TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-HQ-A2OE 
       10.92        19.10        19.82         8.48        22.72        38.60 
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        17.72         1.81 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       50.56        35.97         1.15        15.58        13.48        12.23 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       12.43        86.83        69.34       112.83         3.91        29.56 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI 
        6.21         3.85         6.58        97.12        15.35        79.66 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-AAN0 
       14.93         4.21        11.90        23.64        21.04        56.48 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9RC 
       61.45        86.30        18.15        11.97        13.64        94.29 
TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        88.87        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       63.02        56.35        57.90        19.40        54.21 

$`16P LOSS WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       11.97        94.88       104.65       108.95         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        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI 
       41.75        51.16        66.54        47.80        29.65         2.50 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42         7.33         6.74        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       19.04        12.16        17.88        19.50        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-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-A3MF TCGA-CF-A3MG 
        1.94        23.01        12.79        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       29.79        13.58         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       16.70       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
        7.79         4.80        13.58         8.15         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       163.30 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
       66.05        64.18        53.29        76.60        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       38.24        13.58       166.03        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC 
       15.35        13.64        56.15        11.18        20.32        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       24.03        24.66         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-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-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35        14.96        20.91         3.62        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       19.33         5.36         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG 
        6.28        62.86        18.81         6.15         2.27         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85        12.66        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25        11.08        48.00        15.95        26.93        59.31 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
       33.01         7.23        17.62        66.02         6.94        70.32 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC 
       29.36        21.40        20.71        15.81        19.13        17.75 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q 
        0.49        13.91         3.12        20.98         7.36        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       18.97         7.63        32.78        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF 
       10.65        32.98         7.00        14.27        21.34        20.28 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       36.49        27.35         8.58        19.07         1.51        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       64.01         9.01        12.16        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41Q 
        2.76        15.42        16.27        11.80        52.73        46.98 
TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       44.38        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 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD 
       78.25         3.02        17.82        51.32        45.04        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ 
      125.49         1.87        17.88        48.62        64.80         3.22 
TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SZ 
       15.98        66.41        34.45         5.98        12.76        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-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       98.99        44.32        30.94        27.06        75.39         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        22.36        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       31.20        30.28        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W 
        3.48        58.72        34.06        19.69        59.38        60.16 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41         8.52        19.17         5.52        12.23 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              1.15               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            165.73             166.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             17.98              17.16 
[1] "1.1 - 165.7 (18.0)" "0.1 - 166.0 (17.2)"
[1] "hr=" "1.2"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         1       31        37       37
  16P LOSS WILD-TYPE       1       98       103       98
D69V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                31                 98
  STAGE III               37                103
  STAGE IV                37                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         28  59  11
  16P LOSS WILD-TYPE       95 136  47
D69V4, multiclass
          clus
vv         16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1+T2               28                 95
  T3                     59                136
  T4                     11                 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
  16P LOSS MUTATED    51  15  21   3
  16P LOSS WILD-TYPE 184  32  54   6
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               51                184
  N1               15                 32
  N2               21                 54
  N3                3                  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    40   2
  16P LOSS WILD-TYPE 152   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     40    2
  16P LOSS WILD-TYPE  152    9
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               40                152
  1                2                  9
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    25  82
  16P LOSS WILD-TYPE  82 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     25   82
  16P LOSS WILD-TYPE   82  219
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               25                 82
  MALE                 82                219
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    98   2
  16P LOSS WILD-TYPE 266  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     98    2
  16P LOSS WILD-TYPE  266   17
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                98                266
  YES                2                 17
[1] 2 2
[1] FALSE
D69V9, continuous
D69V10, continuous
D69V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       4                         3    95
  16P LOSS WILD-TYPE    39                        19   232
D69V12, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                3                 19
  WHITE                                   95                232
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  95
  16P LOSS WILD-TYPE   6 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   95
  16P LOSS WILD-TYPE    6  274
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               95                274
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    61  42
  16Q LOSS WILD-TYPE 168 135
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               103                303 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                42                135 
$`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        36.43        12.56        12.92        18.48         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        46.68       142.78        87.32 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P 
        9.67        17.98        67.36        36.66        52.01        15.02 
TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 
      165.73        13.64        12.03        15.35        22.16        25.58 
TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BZ 
        5.52        12.85         7.56        20.91        26.73        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FT-A61P 
        2.70         7.10        12.69        12.36        31.07        11.08 
TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P 
       20.12        15.91        14.07         2.10         2.20        10.92 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-HQ-A2OE TCGA-K4-A3WV 
       14.27        19.10        19.82         8.48        38.60        21.24 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41O 
        9.14         9.07        11.70        17.72         1.81        50.56 
TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       35.97        44.38         1.15        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        69.34       112.83         3.91         3.85 
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-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-AAMG 
       14.93         4.21        11.90        23.64        21.04       110.60 
TCGA-XF-AAML TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3L 
        7.63        56.48        61.45        86.30        18.15        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN 
       13.64        30.28        94.29        64.08        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 
        2.89        19.69         8.61        63.02        56.35        57.90 
TCGA-ZF-AA58 
       54.21 

$`16Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI 
        0.62        51.16        66.54        47.80        29.65         2.50 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42         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        26.14        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-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       28.70        28.41         8.98         1.94        23.01        12.79 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        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-A9FL 
       12.00        12.10        11.34        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 
       13.08         4.90        15.12        29.79        13.58         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-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62        15.62        17.95         7.79         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        8.15         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       163.30        66.05        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S 
       76.60        15.68        50.70        38.24        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       18.81        19.00        15.35        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       20.32        43.59        38.83        29.72         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       24.03        24.66         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-A3SP 
       60.66        24.30        23.41        17.98        29.16        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
       46.78        19.79        27.35        14.96         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-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       18.08        58.92         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
        6.15         2.27         3.06         4.31         9.67        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
       12.66        10.65        17.23         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       48.00        15.95        26.93        59.31        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        70.32        29.36        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       20.71        15.81        19.13        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B 
        8.94        13.91         7.73         3.12        20.98         7.36 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        18.97         7.63        32.78        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QF 
        4.73        10.65        32.98         7.00        21.34        20.28 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       36.49        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40        64.01         9.01        12.16        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
        2.76        27.68        15.42        16.27        11.80        52.73 
TCGA-KQ-A41Q TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       46.98        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 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PH 
       78.25         3.02        29.56        17.82         6.21        51.32 
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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SZ 
       15.98        66.41        34.45         5.98        12.76        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-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
       13.74        92.98        10.82        11.31        54.90        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-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        27.06        75.39         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        22.36        25.41        21.11        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL 
       21.86        28.41        13.41         3.48        58.72        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       34.06        59.38        60.16        35.41        19.40         8.52 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        12.23 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              1.15               0.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            165.73             166.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             17.72              17.16 
[1] "1.1 - 165.7 (17.7)" "0.1 - 166.0 (17.2)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         1       33        30       38
  16Q LOSS WILD-TYPE       1       96       110       97
D70V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                33                 96
  STAGE III               30                110
  STAGE IV                38                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         30  50  15
  16Q LOSS WILD-TYPE       93 145  43
D70V4, multiclass
          clus
vv         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1+T2               30                 93
  T3                     50                145
  T4                     15                 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
  16Q LOSS MUTATED    46  13  23   3
  16Q LOSS WILD-TYPE 189  34  52   6
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               46                189
  N1               13                 34
  N2               23                 52
  N3                3                  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    40   2
  16Q LOSS WILD-TYPE 152   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     40    2
  16Q LOSS WILD-TYPE  152    9
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               40                152
  1                2                  9
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    21  82
  16Q LOSS WILD-TYPE  86 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     21   82
  16Q LOSS WILD-TYPE   86  219
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               21                 86
  MALE                 82                219
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    94   3
  16Q LOSS WILD-TYPE 270  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     94    3
  16Q LOSS WILD-TYPE  270   16
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                94                270
  YES                3                 16
[1] 2 2
[1] FALSE
D70V9, continuous
D70V10, continuous
D70V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       5                         2    92
  16Q LOSS WILD-TYPE    38                        20   235
D70V12, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                2                 20
  WHITE                                   92                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"
D70V13, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5  89
  16Q LOSS WILD-TYPE   4 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   89
  16Q LOSS WILD-TYPE    4  280
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO               89                280
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    96  84
  17P LOSS WILD-TYPE 133  93
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               180                226 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                84                 93 
$`17P LOSS MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA82 TCGA-5N-A9KM TCGA-BL-A0C8 
      104.65       108.95        16.27        51.16        17.42        40.08 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q 
        2.66        12.39        19.04        26.14        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK 
       14.89         8.25        17.16        16.18         4.67         9.96 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG 
       36.43         1.94        12.79        12.56        13.97        12.13 
TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1AB TCGA-DK-A1AD 
       12.16        12.62        18.48         1.84        16.70       112.44 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       46.68        87.32        13.58         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 
       21.30         9.67        66.05        17.98        64.18        50.70 
TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X 
       38.24        13.58       165.73       166.03        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 
       12.03        43.59        15.35        38.83        22.16        25.58 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW 
        0.56        26.96         4.24        24.03         0.92        13.68 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SJ 
       12.95         8.09        16.77         8.94        60.66        24.30 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       29.16         5.52        46.78        12.85         7.56        27.35 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A62O 
       20.91         3.62        26.73         5.36         8.25         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG 
        6.28        13.35        62.86        18.81        12.69         3.06 
TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
       10.85        10.65        61.94        48.00        26.93        59.31 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS 
       20.12        17.62        70.32        21.40        14.07        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        0.49        13.91         2.10         2.20        11.31        18.97 
TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QF TCGA-H4-A2HQ 
        4.73        32.98         7.00        21.34        20.28        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01         9.01        12.16         9.14        11.70        17.72 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41S 
       15.42        11.80        52.73        50.56        46.98         1.15 
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        38.99 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD 
       22.68        76.01        78.25         3.02       112.83        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        6.21         3.85        51.32        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       15.35         1.87        48.62        79.66         3.22        15.98 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SZ 
       14.93         4.21         5.98        12.76        23.64        28.24 
TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
        2.24        10.82        54.90        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-YF-AA3L 
        6.77        44.32        56.48        30.94        86.30        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       13.64        22.36        25.41        31.20        21.86        28.41 
TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        58.72        88.87        47.84        20.22         2.89 
TCGA-ZF-AA4T TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       19.69        60.16        56.35        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 
       24.13        11.97        94.88         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        50.04         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        29.65 
TCGA-5N-A9KI TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        2.50         7.33         6.74         6.58        13.15        12.16 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06        14.96         5.06         8.35        20.48        12.82 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A3MF 
       17.56        28.70        28.41         8.98        23.01        12.59 
TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       13.08        10.95        12.66        12.46        12.10        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
       18.58        13.08        12.92         4.90        15.12         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
       29.79        13.58        21.86         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       19.00       130.88        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3WW 
        7.79       142.78         4.80         8.15        23.21        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       10.55       163.30        53.29        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 
       36.66        52.01        15.02        18.81        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       56.15        11.18        20.32        29.72         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        26.24        24.66         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        12.66        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB 
        8.94         3.25        11.08        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        29.36        20.71        15.81        19.13 
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        32.78        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        36.49 
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-KQ-A41P TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        16.27        35.97        44.38        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
       21.07        13.48        16.54        17.62        37.05        86.83 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI 
       69.34         3.91        29.56        45.04         6.58        17.88 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       64.80        66.41        34.45        11.90        21.04        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-AAMG TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN2 
      110.60        11.31         7.63        71.57        98.99        61.45 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.15         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RD 
        0.66        21.11        30.28        35.84        94.29        13.41 
TCGA-ZF-A9RF TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 
       64.08        34.06         8.61        59.38        63.02        35.41 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21        19.17         5.52        12.23 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.49               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            166.03             163.30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            17.720             16.735 
[1] "0.5 - 166.0 (17.7)" "0.1 - 163.3 (16.7)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         1       50        64       65
  17P LOSS WILD-TYPE       1       79        76       70
D71V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                50                 79
  STAGE III               64                 76
  STAGE IV                65                 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         47  90  28
  17P LOSS WILD-TYPE       76 105  30
D71V4, multiclass
          clus
vv         17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1+T2               47                 76
  T3                     90                105
  T4                     28                 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
  17P LOSS MUTATED    96  20  40   3
  17P LOSS WILD-TYPE 139  27  35   6
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               96                139
  N1               20                 27
  N2               40                 35
  N3                3                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    80   3
  17P LOSS WILD-TYPE 112   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     80    3
  17P LOSS WILD-TYPE  112    8
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               80                112
  1                3                  8
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    51 129
  17P LOSS WILD-TYPE  56 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     51  129
  17P LOSS WILD-TYPE   56  172
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               51                 56
  MALE                129                172
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   160   8
  17P LOSS WILD-TYPE 204  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    160    8
  17P LOSS WILD-TYPE  204   11
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               160                204
  YES                8                 11
[1] 2 2
[1] FALSE
D71V9, continuous
D71V10, continuous
D71V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED      17                        10   141
  17P LOSS WILD-TYPE    26                        12   186
D71V12, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                   17                 26
  BLACK OR AFRICAN AMERICAN               10                 12
  WHITE                                  141                186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4 165
  17P LOSS WILD-TYPE   5 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  165
  17P LOSS WILD-TYPE    5  204
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO              165                204
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    24  19
  17Q LOSS WILD-TYPE 205 158
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                43                363 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                19                158 
$`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        12.79        12.56 
TCGA-CF-A3MI TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A6AV TCGA-DK-AA6Q TCGA-DK-AA76 
       12.16        16.70         8.22        64.18        13.58        12.03 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A97Q TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A43P 
       15.35        38.83         8.09        60.66        12.85        27.35 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A3IE 
       20.91         3.62        13.35        10.85        10.65        20.12 
TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-K4-A4AC TCGA-PQ-A6FN 
       24.92         2.10         7.00        21.34         9.14        16.67 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A9SI 
       12.43        38.99        17.82         6.21         3.85        79.66 
TCGA-XF-A9SP TCGA-XF-AAMX TCGA-ZF-A9R3 TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       14.93         6.77        31.20        47.84        20.22         2.89 
TCGA-ZF-AA4T 
       19.69 

$`17Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04         0.62        41.75        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I 
       10.22        47.80        29.65         2.50        17.42         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-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       26.14        12.16        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25        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        36.43        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
        8.98         1.94        23.01        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       13.08        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.87        18.58        13.08        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       18.48         5.19        29.79         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        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ 
      142.78        87.32         4.80        13.58         8.15        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 
      163.30        66.05        17.98        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       15.68        50.70        36.66        38.24        52.01        15.02 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
      165.73       166.03        18.81        19.00        13.64        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 
       13.64        56.15        11.18        20.32        43.59        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
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-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-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.62        22.52        27.98        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       29.16         5.52        25.74        46.78        19.79         7.56 
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-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-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         7.10         6.28        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-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       31.07        12.66        17.23         8.94         3.25        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        48.00        15.95        26.93        59.31        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        70.32        29.36 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40        20.71        15.81        19.13        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       17.75         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        18.97 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        32.78        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       32.98        14.27        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
       36.49        27.35         8.58        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.40        38.60        64.01         9.01        12.16        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45        21.24         2.76        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       50.56        35.97        46.98        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        21.07        13.48        12.23        14.24         1.84 
TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       16.54        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 
       78.25        69.34         3.02       112.83         3.91        29.56 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       51.32        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-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       15.98        66.41        34.45         4.21         5.98        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-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        18.15 
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-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       22.36        25.41        21.11        30.28        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        94.29        13.41         3.48        64.08        58.72 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       88.87        34.06         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 
       56.35        35.41        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        12.23 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               2.1                0.1 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             79.66             166.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             15.35              17.62 
[1] "2.1 - 79.7 (15.3)"  "0.1 - 166.0 (17.6)"
[1] "hr=" "1.2"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED         1       14        14       14
  17Q LOSS WILD-TYPE       1      115       126      121
D72V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                14                115
  STAGE III               14                126
  STAGE IV                14                121
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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  15  10
  17Q LOSS WILD-TYPE      109 180  48
D72V4, multiclass
          clus
vv         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1+T2               14                109
  T3                     15                180
  T4                     10                 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
  17Q LOSS MUTATED    23   4   7   3
  17Q LOSS WILD-TYPE 212  43  68   6
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               23                212
  N1                4                 43
  N2                7                 68
  N3                3                  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"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    17   1
  17Q LOSS WILD-TYPE 175  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     17    1
  17Q LOSS WILD-TYPE  175   10
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               17                175
  1                1                 10
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    14  29
  17Q LOSS WILD-TYPE  93 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     14   29
  17Q LOSS WILD-TYPE   93  272
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               14                 93
  MALE                 29                272
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    38   3
  17Q LOSS WILD-TYPE 326  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     38    3
  17Q LOSS WILD-TYPE  326   16
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                38                326
  YES                3                 16
[1] 2 2
[1] FALSE
D72V9, continuous
D72V10, continuous
D72V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       5                         4    33
  17Q LOSS WILD-TYPE    38                        18   294
D72V12, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   33                294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  42
  17Q LOSS WILD-TYPE   9 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   42
  17Q LOSS WILD-TYPE    9  327
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               42                327
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    53  46
  18P LOSS WILD-TYPE 176 131
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                99                307 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                46                131 
$`18P LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-4Z-AA7W 
       24.13        94.88       104.65         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        26.14 
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        12.79 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A8HY 
       12.13        13.08        12.16        10.95        12.66        11.34 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB 
        1.84        13.58        21.86         2.14        18.41        16.70 
TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IQ 
      112.44        17.62        46.68        17.95        13.58        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
       50.27        21.30        17.98        64.18        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 
       38.24        15.02       166.03        20.32        43.59        29.72 
TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A7DV TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B7 
        0.56         4.24         1.22        12.95         8.09         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
       24.30        29.16        46.78         7.10        13.35        62.86 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GU-A764 
       20.12        66.02        21.40        14.07        24.92        20.05 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A40E TCGA-HQ-A2OE TCGA-HQ-A2OF 
        4.73        10.65        21.34         8.58        38.60        64.01 
TCGA-K4-A5RI TCGA-KQ-A41P TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G0 TCGA-SY-A9G5 
       11.70        35.97        12.23        16.67        12.43        38.99 
TCGA-UY-A78M TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-AAMR 
       22.68         6.21         3.85        11.90        66.64        91.73 
TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YC-A89H TCGA-YF-AA3L TCGA-YF-AA3M 
        8.32        44.32        86.30        18.84        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM 
       22.36        21.11        28.41        13.41        58.72        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
        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       108.95        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        50.04         0.62        41.75        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM 
       47.80        29.65         2.50        17.42         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        13.15        12.16        17.88        19.50 
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-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        28.70        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A47V 
        1.94        23.01        12.56        13.97        12.59        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-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.87        18.58        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AA 
       15.12        18.48         5.19        29.79        66.41        19.00 
TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
      130.88        16.14        15.62         7.79       142.78        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        4.80         8.15         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       163.30        66.05        53.29        76.60        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6U 
       36.66        52.01        13.58       165.73        18.81        19.00 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 
       13.64        15.35        13.64        56.15        11.18        12.03 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83         0.10        22.16         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
       25.58         0.66        26.96        26.24        24.03        24.66 
TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
        0.92        13.68        14.07        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77         8.94        33.04        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR 
       60.66        23.41        17.98         5.52        25.74        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85         7.56        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-A5BV 
       15.58        26.73        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-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
        6.28        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        12.66 
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        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       48.00        15.95        26.93        59.31        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.62         6.94        70.32        29.36        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       19.13        15.91        17.75         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         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-A766 
       10.92        11.31        18.97         7.63        32.78         5.62 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98         7.00        14.27        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO 
        8.48        36.49        27.35        19.07        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       19.40         9.01        12.16        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        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q 
       15.42        16.27        11.80        52.73        50.56        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       44.38         1.15        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        16.54        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        78.25        69.34         3.02       112.83         3.91 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       29.56        17.82        51.32        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
      125.49        97.12        15.35         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
       64.80        79.66         3.22        15.98        66.41        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY 
       14.93         4.21         5.98        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        18.15         3.88 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        9.63         0.66        25.41        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN 
       21.86        94.29         3.48        64.08        88.87        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        56.35        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        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.56               0.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            166.03             165.73 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             17.98              16.70 
[1] "0.6 - 166.0 (18.0)" "0.1 - 165.7 (16.7)"
[1] "hr=" "1"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         1       30        24       43
  18P LOSS WILD-TYPE       1       99       116       92
D73V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                30                 99
  STAGE III               24                116
  STAGE IV                43                 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 LOSS MUTATED         33  47  14
  18P LOSS WILD-TYPE       90 148  44
D73V4, multiclass
          clus
vv         18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1+T2               33                 90
  T3                     47                148
  T4                     14                 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
  18P LOSS MUTATED    46  12  28   3
  18P LOSS WILD-TYPE 189  35  47   6
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               46                189
  N1               12                 35
  N2               28                 47
  N3                3                  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    53   1
  18P LOSS WILD-TYPE 139  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     53    1
  18P LOSS WILD-TYPE  139   10
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               53                139
  1                1                 10
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    29  70
  18P LOSS WILD-TYPE  78 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     29   70
  18P LOSS WILD-TYPE   78  231
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               29                 78
  MALE                 70                231
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    88   5
  18P LOSS WILD-TYPE 276  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     88    5
  18P LOSS WILD-TYPE  276   14
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                88                276
  YES                5                 14
[1] 2 2
[1] FALSE
D73V9, continuous
D73V10, continuous
D73V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED      11                         4    78
  18P LOSS WILD-TYPE    32                        18   249
D73V12, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                   11                 32
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   78                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"
D73V13, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  87
  18P LOSS WILD-TYPE   6 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   87
  18P LOSS WILD-TYPE    6  282
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               87                282
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    86  60
  18Q LOSS WILD-TYPE 143 117
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               146                260 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                60                117 
$`18Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R 
       24.13        94.88       104.65         8.35        16.27        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM 
       34.98        27.62        51.16        66.54         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T 
       40.08         2.66        19.04        26.14         5.06        14.89 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42C TCGA-CF-A1HR 
        8.35         8.25        17.16        17.56        28.70        12.79 
TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A8HX 
       12.56        12.13        12.16        10.95        12.66        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-CU-A72E 
       11.34        11.87        12.92        15.12         1.84        13.58 
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        46.68 
TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS 
       17.95        87.32         4.80        13.58        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M 
       21.30        66.05        64.18        15.68        50.70        52.01 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A5KE 
       15.02       166.03        15.35        43.59        29.72         0.56 
TCGA-E7-A6MD TCGA-E7-A7DV TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B7 
        4.24         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 
        7.56         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        29.36        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        64.01 
TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI TCGA-KQ-A41P TCGA-KQ-A41S TCGA-LC-A66R 
       25.02        21.24        11.70        35.97         1.15        15.32 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A9PE 
       13.48        12.23        16.67        12.43        38.99         6.21 
TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP 
        3.85         6.58        97.12         3.22        15.98        14.93 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMQ 
       11.90        23.64        66.64       110.60        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M 
       91.73         2.96        44.32        86.30        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RL 
       22.36        21.11        28.41        13.41        58.72        88.87 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 
       47.84         2.89        19.69         8.61        60.16        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA5H 
       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       108.95        44.94        16.83        16.77        50.04 
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        29.65 
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        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47V 
        1.94        23.01        13.97        12.59        13.08        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       18.58        13.08         4.90        18.48         5.19        29.79 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AG 
       21.86        66.41        19.00       130.88        16.14        15.62 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV 
        7.79       142.78         8.15         8.22        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       163.30        17.98        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T 
       67.36        36.66        38.24        13.58       165.73        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 
       19.00        13.64        13.64        56.15        11.18        12.03 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       20.32        15.35        38.83         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       16.70        25.58         0.66        26.96        26.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66         0.92        13.68        14.07        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02         8.94        33.04        12.62        22.52        27.98 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S 
       24.30        23.41        17.98        19.79        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-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       58.92         6.28        18.81         6.15        12.69        12.36 
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-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        11.08        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
       15.95        26.93        59.31        33.01         7.23        17.62 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC 
        6.94        70.32        20.71        15.81        19.13        17.75 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B 
        8.94        13.91         7.73         2.10         3.12         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-AATP TCGA-GU-AATQ 
       10.92        11.31        18.97        32.78        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       14.27        19.82        20.28         8.48        36.49        27.35 
TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
        1.51         9.01        12.16         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       27.68         9.07        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 
       11.80        52.73        50.56        46.98        44.38        15.58 
TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L 
       21.07        14.24         1.84        16.54        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       22.68        86.83        76.01        78.25        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PH TCGA-XF-A8HB 
      112.83         3.91        29.56        17.82        51.32        45.04 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       97.45       125.49        15.35         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SU 
       64.80        79.66        66.41        34.45         4.21         5.98 
TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        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-AAML TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 
        7.63         8.32         6.77        98.99        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        18.15         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        9.63         0.66        25.41        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4R 
       21.86        94.29         3.48        64.08        20.22        34.06 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       59.38        63.02        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.49               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            166.03             165.73 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            17.325             16.800 
[1] "0.5 - 166.0 (17.3)" "0.1 - 165.7 (16.8)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         1       44        47       53
  18Q LOSS WILD-TYPE       1       85        93       82
D74V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                44                 85
  STAGE III               47                 93
  STAGE IV                53                 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
  18Q LOSS MUTATED         42  70  23
  18Q LOSS WILD-TYPE       81 125  35
D74V4, multiclass
          clus
vv         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1+T2               42                 81
  T3                     70                125
  T4                     23                 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
  18Q LOSS MUTATED    78  15  33   4
  18Q LOSS WILD-TYPE 157  32  42   5
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               78                157
  N1               15                 32
  N2               33                 42
  N3                4                  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    73   2
  18Q LOSS WILD-TYPE 119   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     73    2
  18Q LOSS WILD-TYPE  119    9
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               73                119
  1                2                  9
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    42 104
  18Q LOSS WILD-TYPE  65 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     42  104
  18Q LOSS WILD-TYPE   65  197
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               42                 65
  MALE                104                197
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   134   5
  18Q LOSS WILD-TYPE 230  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    134    5
  18Q LOSS WILD-TYPE  230   14
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               134                230
  YES                5                 14
[1] 2 2
[1] FALSE
D74V9, continuous
D74V10, continuous
D74V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED      15                         7   118
  18Q LOSS WILD-TYPE    28                        15   209
D74V12, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                   15                 28
  BLACK OR AFRICAN AMERICAN                7                 15
  WHITE                                  118                209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     5 129
  18Q LOSS WILD-TYPE   4 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5  129
  18Q LOSS WILD-TYPE    4  240
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO              129                240
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    49  45
  19P LOSS WILD-TYPE 180 132
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                94                312 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                45                132 
$`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        36.43         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        15.35        43.59 
TCGA-E7-A4IJ TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3SJ TCGA-FD-A3SM 
       22.16        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         7.56         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        11.08        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 
       29.36        20.71        19.13         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-KQ-A41Q TCGA-KQ-A41S 
        9.01        25.02        27.68        17.72        46.98         1.15 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G5 
       15.32        13.48        12.23        16.67        14.24        38.99 
TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A9SG 
       22.68       112.83        17.82         3.85        45.04        48.62 
TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 
        3.22        34.45         4.21        11.90        66.64         2.10 
TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC 
      110.60         6.77        86.30        13.64        30.28        94.29 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5H 
       88.87        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 
       24.13        11.97        94.88       104.65       108.95        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        50.04 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       47.80        29.65         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        2.66         6.74        12.39         6.58        13.15        26.14 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       12.16        17.88        19.50        14.89        14.96         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F0 
        8.25        17.16        12.82        28.70        28.41         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        18.58        13.08         4.90        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.19        29.79         1.84        13.58        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62        46.68        17.95         7.79       142.78         4.80 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        8.15        50.27        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      163.30        66.05        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       15.68        50.70        36.66        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       13.58       165.73       166.03        18.81        19.00        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        56.15        11.18        12.03        20.32        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83        29.72         0.10         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
       24.66         0.92         1.22        13.68        14.07        15.32 
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-A3SL TCGA-FD-A3SN TCGA-FD-A3SP 
       22.52        27.98        60.66        23.41        29.16        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       46.78        19.79        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-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
        2.70         7.10         6.28        13.35        62.86         6.15 
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-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       31.07        12.66         3.25        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3BM 
       26.93        59.31        17.62        66.02        70.32        21.40 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 
       15.81        15.91        14.07        17.75        24.92        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42R 
        7.73         2.10         3.12        20.98         7.36        18.97 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
       32.78        20.05         5.62         4.73        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        21.34        19.10        20.28         8.48        36.49 
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-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       64.01        12.16         3.45        21.24         2.76         9.14 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        9.07        11.70         1.81        15.42        16.27        11.80 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       52.73        50.56        35.97        44.38        15.58        21.07 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
        1.84        16.54        12.43        17.62        37.05        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       76.01        78.25        69.34         3.02         3.91        29.56 
TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        6.21        51.32         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-A9SK 
       15.35         1.87        17.88        64.80        79.66        15.98 
TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY 
       66.41        14.93         5.98        12.76        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-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-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-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        61.45        27.06        75.39        18.15         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        22.36        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       21.11        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        64.08        58.72        47.84        20.22         2.89 
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        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        19.40         8.52        54.21         5.52        12.23 

  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 
             16.95              17.29 
[1] "0.5 - 112.8 (17.0)" "0.1 - 166.0 (17.3)"
[1] "hr=" "1.2"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         0       21        35       38
  19P LOSS WILD-TYPE       2      108       105       97
D75V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                21                108
  STAGE III               35                105
  STAGE IV                38                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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  56  11
  19P LOSS WILD-TYPE      103 139  47
D75V4, multiclass
          clus
vv         19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1+T2               20                103
  T3                     56                139
  T4                     11                 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
  19P LOSS MUTATED    46  14  19   4
  19P LOSS WILD-TYPE 189  33  56   5
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               46                189
  N1               14                 33
  N2               19                 56
  N3                4                  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"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    36   4
  19P LOSS WILD-TYPE 156   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     36    4
  19P LOSS WILD-TYPE  156    7
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               36                156
  1                4                  7
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    25  69
  19P LOSS WILD-TYPE  82 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     25   69
  19P LOSS WILD-TYPE   82  232
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               25                 82
  MALE                 69                232
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    87   1
  19P LOSS WILD-TYPE 277  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     87    1
  19P LOSS WILD-TYPE  277   18
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                87                277
  YES                1                 18
[1] 2 2
[1] FALSE
D75V9, continuous
D75V10, continuous
D75V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       4                         5    79
  19P LOSS WILD-TYPE    39                        17   248
D75V12, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                   79                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"
D75V13, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     4  84
  19P LOSS WILD-TYPE   5 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   84
  19P LOSS WILD-TYPE    5  285
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO               84                285
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    29  28
  19Q LOSS WILD-TYPE 200 149
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                57                349 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                28                149 
$`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        15.35        22.16        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        11.08        33.01         7.23        20.12 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A4ZW TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-AATO 
       20.71        19.13         0.49         2.20         7.63        10.65 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       27.68        17.72         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OD TCGA-XF-A9SG 
       12.23        16.67        38.99        22.68       112.83        48.62 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG 
       34.45         4.21        11.90        66.64         2.10       110.60 
TCGA-XF-AAML TCGA-ZF-A9R4 TCGA-ZF-AA5H 
        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 
       24.13        11.97        94.88       104.65       108.95        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        50.04 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       47.80        29.65         2.50        17.42        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-A20T TCGA-BT-A20U 
       26.14        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PJ 
        5.06         8.35         8.25        17.16        16.18        12.82 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       28.70        36.43        28.41         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
       18.58        13.08         4.90        15.12        18.48         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       29.79         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62        46.68        17.95         7.79       142.78        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
        4.80        13.58         8.15        50.27        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       163.30        66.05        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       76.60        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T 
       52.01        15.02        13.58       165.73       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 
       19.00        13.64        13.64        56.15        11.18        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       20.32        43.59        15.35        38.83        29.72         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        25.58         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.24         4.24        24.03        24.66         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       13.68        14.07        15.32        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-A3SP TCGA-FD-A3SQ 
       24.30        23.41        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         7.56        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-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        5.69        27.45        18.08         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-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07        12.66 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       17.23         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       59.31        17.62        66.02         6.94        70.32        29.36 
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-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-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 
        7.36        10.92        11.31        18.97        32.78        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62         4.73        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        36.49        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 
       64.01         9.01        12.16        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.76         9.14         9.07        11.70         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       16.27        11.80        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       44.38        21.07        14.24         1.84        16.54        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        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
        3.02         3.91        29.56        17.82         6.21         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       51.32        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-A9SK TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SX 
       15.98        66.41        14.93         5.98        12.76        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-AAMJ TCGA-XF-AAMQ 
       13.74        92.98        10.82        11.31        54.90        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 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       13.64        22.36        25.41        21.11        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        94.29        13.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       58.72        88.87        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        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       35.41        57.90        19.40         8.52        54.21         5.52 
TCGA-ZF-AA5P 
       12.23 

  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 
             14.37              17.62 
[1] "0.5 - 112.8 (14.4)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         0       16        22       19
  19Q LOSS WILD-TYPE       2      113       118      116
D76V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                16                113
  STAGE III               22                118
  STAGE IV                19                116
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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  32   8
  19Q LOSS WILD-TYPE      111 163  50
D76V4, multiclass
          clus
vv         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1+T2               12                111
  T3                     32                163
  T4                      8                 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
  19Q LOSS MUTATED    30   6  11   2
  19Q LOSS WILD-TYPE 205  41  64   7
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               30                205
  N1                6                 41
  N2               11                 64
  N3                2                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    21   2
  19Q LOSS WILD-TYPE 171   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     21    2
  19Q LOSS WILD-TYPE  171    9
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               21                171
  1                2                  9
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    15  42
  19Q LOSS WILD-TYPE  92 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     15   42
  19Q LOSS WILD-TYPE   92  259
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               15                 92
  MALE                 42                259
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    52   1
  19Q LOSS WILD-TYPE 312  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     52    1
  19Q LOSS WILD-TYPE  312   18
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                52                312
  YES                1                 18
[1] 2 2
[1] FALSE
D76V9, continuous
D76V10, continuous
D76V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       4                         2    49
  19Q LOSS WILD-TYPE    39                        20   278
D76V12, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                2                 20
  WHITE                                   49                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"
D76V13, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2  51
  19Q LOSS WILD-TYPE   7 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   51
  19Q LOSS WILD-TYPE    7  318
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               51                318
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    14  19
  20P LOSS WILD-TYPE 215 158
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                33                373 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                19                158 
$`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        26.14        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         8.15         9.67        66.05        64.18 
TCGA-E7-A6MD TCGA-E7-A85H TCGA-FD-A5C0 TCGA-FD-A6TB TCGA-G2-A3VY TCGA-G2-AA3D 
        4.24        12.95        18.08        18.81        17.62        70.32 
TCGA-GU-A42R TCGA-GU-AATQ TCGA-GV-A40E TCGA-HQ-A2OE TCGA-K4-A4AC TCGA-UY-A78K 
       18.97         7.00         8.58        38.60         9.14        17.62 
TCGA-UY-A78N TCGA-XF-A8HE TCGA-XF-A9SW TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAN7 
       86.83       125.49        11.90         7.63         6.77        18.15 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       28.41        13.41        64.08 

$`20P LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       10.22        47.80        29.65         2.50        17.42        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-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       12.16        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        36.43        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        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V 
       12.59        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.87        18.58        13.08        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
       18.48         5.19        29.79         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        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ 
      142.78        87.32         4.80        13.58         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       163.30 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       17.98        53.29        76.60        67.36        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       36.66        38.24        52.01        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        18.81        19.00        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       56.15        11.18        12.03        20.32        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         0.10        22.16         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       25.58         0.56         0.66        26.96        26.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
       24.66         0.92         1.22        13.68        14.07        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         7.56        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-A5C1 TCGA-FD-A62N 
        5.36         5.69         8.25        27.45        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-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-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       31.07        12.66        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 
       11.08        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       33.01         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       21.40        20.71        15.81        19.13        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-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31         7.63        32.78        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       10.65        32.98        14.27        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
       20.28         8.48        36.49        27.35        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51        19.40        64.01         9.01        12.16        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45        21.24         2.76        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       50.56        35.97        46.98        44.38         1.15        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-A78L TCGA-UY-A78M 
        1.84        16.54        12.43        38.99        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       76.01        78.25        69.34         3.02       112.83         3.91 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
       29.56        17.82         6.21         3.85        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
        6.58        97.45        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL 
       48.62        64.80        79.66         3.22        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SX 
       34.45        14.93         4.21         5.98        12.76        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-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       11.31        54.90        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-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-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       11.97        13.64        22.36        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RG 
       30.28        35.84        21.86        94.29         3.48        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       88.87        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        56.35        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        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              4.24               0.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            125.49             166.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             17.88              16.83 
[1] "4.2 - 125.5 (17.9)" "0.1 - 166.0 (16.8)"
[1] "hr=" "1.3"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         0       12         9       11
  20P LOSS WILD-TYPE       2      117       131      124
D77V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                12                117
  STAGE III                9                131
  STAGE IV                11                124
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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   2
  20P LOSS WILD-TYPE      112 179  56
D77V4, multiclass
          clus
vv         20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1+T2               11                112
  T3                     16                179
  T4                      2                 56
[1] 3 2
[1] TRUE
[1] "dimension of 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   3   9   0
  20P LOSS WILD-TYPE 218  44  66   9
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               17                218
  N1                3                 44
  N2                9                 66
  N3                0                  9
[1] 4 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    14   0
  20P LOSS WILD-TYPE 178  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     14    0
  20P LOSS WILD-TYPE  178   11
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               14                178
  1                0                 11
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     5  28
  20P LOSS WILD-TYPE 102 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5   28
  20P LOSS WILD-TYPE  102  273
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                5                102
  MALE                 28                273
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    27   2
  20P LOSS WILD-TYPE 337  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     27    2
  20P LOSS WILD-TYPE  337   17
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                27                337
  YES                2                 17
[1] 2 2
[1] FALSE
D77V9, continuous
D77V10, continuous
D77V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       6                         1    24
  20P LOSS WILD-TYPE    37                        21   303
D77V12, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    6                 37
  BLACK OR AFRICAN AMERICAN                1                 21
  WHITE                                   24                303
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  30
  20P LOSS WILD-TYPE   9 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   30
  20P LOSS WILD-TYPE    9  339
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               30                339
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     5   9
  20Q LOSS WILD-TYPE 224 168
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                14                392 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                168 
$`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-E7-A6MD TCGA-UY-A78N TCGA-XF-A9SW TCGA-XF-AAML TCGA-XF-AAMW 
        9.67         4.24        86.83        11.90         7.63         8.32 
TCGA-XF-AAN7 TCGA-ZF-A9RF 
       18.15        64.08 

$`20Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       10.22        47.80        29.65         2.50        17.42        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-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       19.04        26.14        12.16        19.50         5.06        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        36.43 
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        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM 
       12.00        12.10        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90        15.12        18.48         5.19        29.79 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84        13.58         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-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       46.68        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        8.15         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       20.81        10.55       163.30        66.05        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S 
       38.24        52.01        15.02        13.58       165.73       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       18.81        19.00        13.64        15.35        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       11.18        12.03        20.32        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       29.72         0.10        22.16         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24        24.03        24.66 
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         7.56        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-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-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07        12.66        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        11.08        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        59.31        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        70.32        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81        19.13        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-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
       20.98         2.20         7.36        10.92        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
        7.63        32.78        20.05         5.62         4.73        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        36.49        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        64.01         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       12.16        25.02         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        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       16.27        11.80        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       44.38         1.15        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        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
       38.99        17.62        37.05        22.68        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       69.34         3.02       112.83         3.91        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
        6.21         3.85        51.32        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
      125.49        97.12        15.35         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
       64.80        79.66         3.22        15.98        66.41        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY 
       14.93         4.21         5.98        12.76        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-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY 
       54.90        71.57        91.73         2.96         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-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        22.36        25.41        21.11        31.20        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       35.84        21.86        28.41        94.29        13.41         3.48 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       58.72        88.87        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        56.35 
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        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              4.24               0.10 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             87.32             166.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            14.890             17.195 
[1] "4.2 - 87.3 (14.9)"  "0.1 - 166.0 (17.2)"
[1] "hr=" "1.6"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         0        5         1        8
  20Q LOSS WILD-TYPE       2      124       139      127
D78V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                 5                124
  STAGE III                1                139
  STAGE IV                 8                127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  20Q LOSS MUTATED          7   4   2
  20Q LOSS WILD-TYPE      116 191  56
D78V4, multiclass
          clus
vv         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1+T2                7                116
  T3                      4                191
  T4                      2                 56
[1] 3 2
[1] TRUE
[1] "dimension of 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   4   3   0
  20Q LOSS WILD-TYPE 230  43  72   9
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                5                230
  N1                4                 43
  N2                3                 72
  N3                0                  9
[1] 4 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     9   0
  20Q LOSS WILD-TYPE 183  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      9    0
  20Q LOSS WILD-TYPE  183   11
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                9                183
  1                0                 11
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3  11
  20Q LOSS WILD-TYPE 104 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3   11
  20Q LOSS WILD-TYPE  104  290
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                3                104
  MALE                 11                290
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    12   0
  20Q LOSS WILD-TYPE 352  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     12    0
  20Q LOSS WILD-TYPE  352   19
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                12                352
  YES                0                 19
[1] 2 2
[1] FALSE
D78V9, continuous
D78V10, continuous
D78V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       1                         1    12
  20Q LOSS WILD-TYPE    42                        21   315
D78V12, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    1                 42
  BLACK OR AFRICAN AMERICAN                1                 21
  WHITE                                   12                315
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  13
  20Q LOSS WILD-TYPE   9 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   13
  20Q LOSS WILD-TYPE    9  356
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               13                356
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    40  39
  21Q LOSS WILD-TYPE 189 138
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                79                327 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                39                138 
$`21Q LOSS MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13J 
       24.13         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        36.43        12.79        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        36.66 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 
       13.58       165.73        13.64        15.35        13.64        12.03 
TCGA-E5-A2PC TCGA-E7-A6MD TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43X 
       43.59         4.24         8.94        23.41         5.52         3.62 
TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TF 
       15.58         5.36         8.25        62.86        12.69         2.27 
TCGA-FD-A6TK TCGA-G2-A2EJ TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3YS TCGA-GC-A6I1 
       10.85        48.00        70.32        29.36        24.92         8.94 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A6ZA TCGA-HQ-A2OF TCGA-HQ-A5ND 
        4.73        14.27        36.49        22.72        64.01         9.01 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-KQ-A41O TCGA-LT-A5Z6 
        2.76         9.14        11.70        17.72        50.56        15.58 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       76.01        78.25        69.34       112.83         3.91        29.56 
TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMG 
       15.35        79.66        23.64        66.64        13.74       110.60 
TCGA-XF-AAML TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
        7.63        61.45        18.15        22.36        21.86        13.41 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4W TCGA-ZF-AA53 TCGA-ZF-AA56 
       20.22         2.89        34.06        60.16        57.90         8.52 
TCGA-ZF-AA5H 
       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        94.88       104.65       108.95         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 
       50.04        41.75        66.54        15.12        47.80        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
        2.50        17.42         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        26.14        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06        14.96         8.35        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-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        8.98         1.94        23.01        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       18.48        29.79        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        46.68        17.95         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32         4.80        13.58         8.15        50.27        21.30 
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       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T 
       50.70        38.24        52.01        15.02       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       19.00        56.15        11.18        20.32        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       29.72         0.10        22.16         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24        24.03        24.66 
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-A3B6 TCGA-FD-A3B7 
       14.37         8.09        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-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-A43N 
       29.16        25.74        46.78        19.79        12.85         7.56 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35        14.96        20.91        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
       19.33         5.69        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        7.10         6.28        13.35        18.81         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        3.06         4.31         9.67        31.07        12.66        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK 
       17.23         8.94         3.25        11.08        61.94        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       26.93        59.31        33.01         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       66.02         6.94        21.40        20.71        15.81        19.13 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.91        14.07        17.75         0.49        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        18.97         7.63        32.78        20.05         5.62 
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-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-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       19.40        38.60        12.16        25.02         3.45        21.24 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       27.68         9.07         1.81        15.42        16.27        11.80 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       52.73        35.97        46.98        44.38         1.15        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-A78L TCGA-UY-A78M 
       16.54        12.43        38.99        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
       86.83         3.02        17.82         6.21         3.85        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH 
       45.04         6.58        97.45       125.49        97.12         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL 
       17.88        48.62        64.80         3.22        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       34.45        14.93         4.21         5.98        12.76        11.90 
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-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
        2.10        92.98        10.82        11.31        54.90        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-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       56.48        30.94        86.30        27.06        75.39         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        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       21.11        31.20        30.28        35.84        28.41        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4T 
        3.48        64.08        58.72        88.87        47.84        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
        8.61        59.38        63.02        56.35        35.41        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21         5.52        12.23 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.62               0.10 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            165.73             166.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             15.35              17.56 
[1] "0.6 - 165.7 (15.3)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.2"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         1       23        24       31
  21Q LOSS WILD-TYPE       1      106       116      104
D79V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                23                106
  STAGE III               24                116
  STAGE IV                31                104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  21Q LOSS MUTATED         21  39  12
  21Q LOSS WILD-TYPE      102 156  46
D79V4, multiclass
          clus
vv         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1+T2               21                102
  T3                     39                156
  T4                     12                 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
  21Q LOSS MUTATED    40  20  11   0
  21Q LOSS WILD-TYPE 195  27  64   9
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               40                195
  N1               20                 27
  N2               11                 64
  N3                0                  9
[1] 4 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    35   2
  21Q LOSS WILD-TYPE 157   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     35    2
  21Q LOSS WILD-TYPE  157    9
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               35                157
  1                2                  9
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    22  57
  21Q LOSS WILD-TYPE  85 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     22   57
  21Q LOSS WILD-TYPE   85  244
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               22                 85
  MALE                 57                244
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    73   3
  21Q LOSS WILD-TYPE 291  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     73    3
  21Q LOSS WILD-TYPE  291   16
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                73                291
  YES                3                 16
[1] 2 2
[1] FALSE
D79V9, continuous
D79V10, continuous
D79V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       3                         5    68
  21Q LOSS WILD-TYPE    40                        17   259
D79V12, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    3                 40
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                   68                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"
D79V13, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2  71
  21Q LOSS WILD-TYPE   7 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   71
  21Q LOSS WILD-TYPE    7  298
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               71                298
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    88  71
  22Q LOSS WILD-TYPE 141 106
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               159                247 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                71                106 
$`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-A3MI TCGA-CF-A47X 
       36.43         8.98         1.94        23.01        12.16        12.62 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I1 
       12.92        18.48         5.19        18.41        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
        7.79       142.78        13.58         8.15         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       21.30         9.67        17.98        67.36        15.68        50.70 
TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA6X 
       52.01        13.58       165.73       166.03        13.64        15.35 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A5KE TCGA-E7-A6ME 
       11.18        12.03        43.59        15.35         0.56        24.03 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
        1.22        13.68        32.02        16.77         8.94        33.04 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS 
       22.52        24.30        29.16         5.52        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
        7.56        20.91        15.58         5.36         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08         2.70         6.28        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
       12.36         2.27        10.85        31.07        17.23        11.08 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A6I1 
        7.23        20.12        17.62        15.91        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
       13.91         7.73         2.10         2.20         7.36        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP 
       18.97         7.63        20.05         5.62        10.65        32.98 
TCGA-GV-A3JX TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.10        19.07        22.72        19.40        12.16        25.02 
TCGA-K4-A3WU TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        3.45         9.07        11.70        17.72         1.81        15.42 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 
        1.15        15.32        13.48        12.23        16.67        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       17.62        37.05        86.83        69.34         3.91        29.56 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG 
        6.21         3.85        45.04         6.58        97.12        15.35 
TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW 
       48.62         3.22        15.98        34.45         4.21        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMF 
       23.64        21.04        28.24        26.27         2.24        10.82 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
      110.60         2.96        44.32        56.48        61.45        86.30 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       11.97        13.64        21.86        28.41        94.29        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
        3.48        47.84        20.22        34.06        19.69         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
       63.02        35.41        19.17 

$`22Q LOSS WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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        50.04        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        15.12        29.65         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        7.33         6.74        12.39         6.58        13.15        26.14 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50        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-A42F TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       12.82         9.96        28.41        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.59        12.13        13.08        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-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
       29.79         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         4.80        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       163.30        66.05        64.18        53.29        76.60 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA71 
       36.66        38.24        15.02        18.81        19.00        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       56.15        20.32        38.83        29.72         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70        25.58         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        4.24        24.66         0.92        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       14.37         8.09         4.01        12.62        27.98        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S 
       23.41        17.98        25.74        46.78        27.35        14.96 
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-A5C1 TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FD-A6TH 
       58.92         7.10        13.35        62.86         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
        9.67        12.66        10.65         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B 
       48.00        15.95        26.93        59.31        33.01        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        70.32        29.36        21.40        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A3OQ TCGA-GD-A3OS 
       19.13        14.07        17.75         0.49         3.12        20.98 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       10.92        32.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        36.49        27.35         8.58 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-K4-A4AB 
        1.51        38.60        64.01         9.01        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
        9.14        27.68        16.27        11.80        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-R3-A69X 
       35.97        46.98        44.38        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        16.54        12.43        22.68        76.01        78.25 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
        3.02       112.83        17.82        51.32        97.45       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SP 
        1.87        17.88        64.80        79.66        66.41        14.93 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
        5.98        12.76        18.90        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        92.98        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN4 
       91.73         8.32         6.77        98.99        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.15         3.88        18.84         9.63         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       22.36        25.41        21.11        31.20        30.28        35.84 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W 
       64.08        58.72        88.87         2.89        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       56.35        57.90        19.40         8.52        54.21         5.52 
TCGA-ZF-AA5P 
       12.23 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.56               0.10 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            166.03             163.30 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             16.27              17.82 
[1] "0.6 - 166.0 (16.3)" "0.1 - 163.3 (17.8)"
[1] "hr=" "1.2"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         0       41        53       65
  22Q LOSS WILD-TYPE       2       88        87       70
D80V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                41                 88
  STAGE III               53                 87
  STAGE IV                65                 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
  22Q LOSS MUTATED         39  80  27
  22Q LOSS WILD-TYPE       84 115  31
D80V4, multiclass
          clus
vv         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1+T2               39                 84
  T3                     80                115
  T4                     27                 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
  22Q LOSS MUTATED    79  20  41   3
  22Q LOSS WILD-TYPE 156  27  34   6
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               79                156
  N1               20                 27
  N2               41                 34
  N3                3                  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"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    56   3
  22Q LOSS WILD-TYPE 136   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     56    3
  22Q LOSS WILD-TYPE  136    8
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               56                136
  1                3                  8
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    42 117
  22Q LOSS WILD-TYPE  65 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     42  117
  22Q LOSS WILD-TYPE   65  184
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               42                 65
  MALE                117                184
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   142   5
  22Q LOSS WILD-TYPE 222  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    142    5
  22Q LOSS WILD-TYPE  222   14
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               142                222
  YES                5                 14
[1] 2 2
[1] FALSE
D80V9, continuous
D80V10, continuous
D80V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       8                         8   135
  22Q LOSS WILD-TYPE    35                        14   192
D80V12, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    8                 35
  BLACK OR AFRICAN AMERICAN                8                 14
  WHITE                                  135                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     7 140
  22Q LOSS WILD-TYPE   2 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7  140
  22Q LOSS WILD-TYPE    2  229
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  2
  NOT HISPANIC OR LATINO              140                229
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    40  31
  XP LOSS WILD-TYPE 189 146
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               71               335 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               31               146 
$`XP LOSS MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA84 TCGA-5N-A9KI 
      104.65       108.95         8.35        16.83        15.12         2.50 
TCGA-BT-A20T TCGA-BT-A3PH TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH 
       14.89         4.67        17.56        13.97        12.13        13.08 
TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AB 
       12.62        12.10        12.92         5.19         2.14        16.70 
TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6B5 TCGA-DK-AA6L 
       87.32        50.27        21.30         9.67        50.70        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 
       13.58        18.81        13.64        12.03        43.59        29.72 
TCGA-E7-A7DU TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS 
        0.92        16.77        33.04        29.16        19.79        12.85 
TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TF TCGA-G2-A2EL 
       15.58         8.25         2.70         6.15         2.27        26.93 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A4ZW TCGA-GD-A6C6 TCGA-GV-A3JX 
        7.23        17.62        29.36         0.49         2.20        19.10 
TCGA-GV-A40G TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO 
       19.07        64.01        21.24        17.72         1.81        11.80 
TCGA-KQ-A41O TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78P 
       50.56        15.58        12.23         1.84        16.54        78.25 
TCGA-UY-A8OD TCGA-XF-A8HF TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SZ TCGA-XF-AAML 
      112.83        97.12        34.45        14.93        28.24         7.63 
TCGA-XF-AAMT TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4U 
        2.96        28.41        88.87        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 
       24.13        11.97        94.88        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        50.04         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80        29.65        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         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        26.14        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E 
       16.18        20.48        12.82         9.96        28.70        36.43 
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        12.79        12.56 
TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.59        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.26        13.12        12.00        11.34        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
       18.58        13.08         4.90        15.12        18.48        29.79 
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-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        46.68 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
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       163.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       66.05        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S 
       15.68        36.66        52.01        15.02       165.73       166.03 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
       19.00        15.35        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83         0.10        22.16         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       25.58         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       24.03        24.66         1.22        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 
       15.32        14.37         8.09        32.02         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-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P 
       17.98         5.52        25.74        46.78         7.56        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        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-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-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.36         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 
       12.66        10.65        17.23         8.94         3.25        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
       61.94        48.00        15.95        59.31        33.01        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       66.02         6.94        70.32        21.40        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       19.13        15.91        14.07        17.75        24.92         8.94 
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-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        18.97         7.63        32.78        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-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.82        20.28         8.48        36.49        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND 
        8.58        22.72         1.51        19.40        38.60         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       12.16        25.02         3.45         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41P 
        9.07        11.70        15.42        16.27        52.73        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V 
       46.98        44.38         1.15        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        38.99        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        69.34         3.02         3.91 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
       29.56        17.82         6.21         3.85        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
        6.58        97.45       125.49        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL 
       48.62        64.80        79.66         3.22        15.98        66.41 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        4.21         5.98        12.76        11.90        23.64        21.04 
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-AAMZ 
       71.57        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 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        22.36        25.41        21.11        31.20        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       35.84        21.86        94.29        13.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89        19.69        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        56.35        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21        19.17         5.52        12.23 

  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 
            15.58             17.72 
[1] "0.5 - 112.8 (15.6)" "0.1 - 166.0 (17.7)"
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP LOSS MUTATED         0       26        24       21
  XP LOSS WILD-TYPE       2      103       116      114
D81V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               26               103
  STAGE III              24               116
  STAGE IV               21               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
  XP LOSS MUTATED         21  32  10
  XP LOSS WILD-TYPE      102 163  48
D81V4, multiclass
          clus
vv         XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1+T2              21               102
  T3                    32               163
  T4                    10                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
  XP LOSS MUTATED    42  10  10   1
  XP LOSS WILD-TYPE 193  37  65   8
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              42               193
  N1              10                37
  N2              10                65
  N3               1                 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"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    30   2
  XP LOSS WILD-TYPE 162   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     30    2
  XP LOSS WILD-TYPE  162    9
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              30               162
  1               2                 9
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    17  54
  XP LOSS WILD-TYPE  90 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     17   54
  XP LOSS WILD-TYPE   90  247
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              17                90
  MALE                54               247
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    62   5
  XP LOSS WILD-TYPE 302  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     62    5
  XP LOSS WILD-TYPE  302   14
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               62               302
  YES               5                14
[1] 2 2
[1] FALSE
D81V9, continuous
D81V10, continuous
D81V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       7                         5    56
  XP LOSS WILD-TYPE    36                        17   271
D81V12, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   7                36
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                  56               271
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2  64
  XP LOSS WILD-TYPE   7 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   64
  XP LOSS WILD-TYPE    7  305
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              64               305
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    50  30
  XQ LOSS WILD-TYPE 179 147
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               80               326 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               30               147 
$`XQ LOSS MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA80 TCGA-4Z-AA84 
      104.65       108.95         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-A3MG 
       14.89        16.18         4.67        17.56        13.97        12.13 
TCGA-CF-A3MH TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AB 
       13.08        12.62        12.10         5.19         2.14        16.70 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6B5 
      130.88        87.32        50.27        21.30         9.67        50.70 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        18.81        13.64        13.64        12.03        43.59 
TCGA-E7-A3X6 TCGA-E7-A7DU TCGA-E7-A85H TCGA-FD-A3B4 TCGA-FD-A3SN TCGA-FD-A3SR 
       29.72         0.92        12.95        16.77        29.16        19.79 
TCGA-FD-A3SS TCGA-FD-A5BY TCGA-FD-A62N TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A2EL 
       12.85         8.25         2.70        31.07         3.25        26.93 
TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A4ZW TCGA-GD-A6C6 TCGA-GU-A42P 
        7.23        66.02        29.36         0.49         2.20        10.92 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A40G TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV 
       19.10        36.49        19.07        38.60        64.01        21.24 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41O TCGA-LT-A5Z6 
       27.68        17.72         1.81        11.80        50.56        15.58 
TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
       12.23         1.84        16.54        78.25       112.83        17.82 
TCGA-UY-A9PF TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SP TCGA-XF-A9SZ TCGA-XF-AAMG 
        3.85        97.12        17.88        14.93        28.24       110.60 
TCGA-XF-AAMT TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-A9RM 
        2.96        18.15        11.97        28.41        88.87        47.84 
TCGA-ZF-AA4R TCGA-ZF-AA4U 
       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 
       24.13        11.97        94.88        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        50.04        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       66.54        10.22        47.80        29.65         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         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        26.14        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.96         5.06         8.35         8.25        17.16 
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        36.43        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF 
        8.98         1.94        23.01        12.79        12.56        12.59 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       12.16        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-A9FL 
       13.12        12.00        11.34        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
       13.08        12.92         4.90        15.12        18.48        29.79 
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-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        7.79       142.78         4.80        13.58         8.15         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       17.72        23.21        20.81        10.55       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S 
       36.66        38.24        52.01        15.02       165.73       166.03 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       19.00        15.35        56.15        11.18        20.32        15.35 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83         0.10        22.16         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66         1.22        13.68        14.07        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        8.09        32.02         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-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
        5.52        25.74        46.78         7.56        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-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-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P 
       10.85        12.66        10.65        17.23         8.94        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
       61.94        48.00        15.95        59.31        33.01        20.12 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.62         6.94        70.32        21.40        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       19.13        15.91        14.07        17.75        24.92         8.94 
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-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        18.97         7.63        32.78        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-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
       19.82        20.28         8.48        27.35         8.58        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        1.51        19.40         9.01        12.16        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P 
        2.76         9.14         9.07        11.70        15.42        16.27 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       52.73        35.97        46.98        44.38         1.15        15.32 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 
       21.07        13.48        16.67        14.24        12.43        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HB 
        3.02         3.91        29.56         6.21        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG 
        6.58        97.45       125.49        15.35         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
       64.80        79.66         3.22        15.98        66.41        34.45 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        4.21         5.98        12.76        11.90        23.64        21.04 
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-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       13.74        92.98        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       71.57        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-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        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       25.41        21.11        31.20        30.28        35.84        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN 
       94.29        13.41         3.48        64.08        58.72        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89        19.69        59.38        60.16        63.02        56.35 
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        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  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 
           16.735            17.520 
[1] "0.5 - 130.9 (16.7)" "0.1 - 166.0 (17.5)"
[1] "hr=" "1.2"
D82V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         0       29        26       24
  XQ LOSS WILD-TYPE       2      100       114      111
D82V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               29               100
  STAGE III              26               114
  STAGE IV               24               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
  XQ LOSS MUTATED         27  36  10
  XQ LOSS WILD-TYPE       96 159  48
D82V4, multiclass
          clus
vv         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1+T2              27                96
  T3                    36               159
  T4                    10                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
  XQ LOSS MUTATED    49  11  13   1
  XQ LOSS WILD-TYPE 186  36  62   8
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              49               186
  N1              11                36
  N2              13                62
  N3               1                 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"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    36   1
  XQ LOSS WILD-TYPE 156  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     36    1
  XQ LOSS WILD-TYPE  156   10
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              36               156
  1               1                10
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    19  61
  XQ LOSS WILD-TYPE  88 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     19   61
  XQ LOSS WILD-TYPE   88  240
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              19                88
  MALE                61               240
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    70   5
  XQ LOSS WILD-TYPE 294  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     70    5
  XQ LOSS WILD-TYPE  294   14
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               70               294
  YES               5                14
[1] 2 2
[1] FALSE
D82V9, continuous
D82V10, continuous
D82V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       7                         5    63
  XQ LOSS WILD-TYPE    36                        17   264
D82V12, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   7                36
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                  63               264
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V13, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4  68
  XQ LOSS WILD-TYPE   5 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4   68
  XQ LOSS WILD-TYPE    5  301
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO              68               301
[1] 2 2
[1] FALSE
