[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/22506467/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/22507732/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 
               89               319 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               89               319 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              126               282 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              126               282 
[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 
               55               353 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               55               353 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              143               265 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              143               265 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              179               229 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              179               229 
[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 
               51               357 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               51               357 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               73               335 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               73               335 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               39               369 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               39               369 
[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 
              148               260 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              148               260 
[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 
              200               208 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              200               208 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               69               339 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               69               339 
[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 
               117                291 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               117                291 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                44                364 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                44                364 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                29                379 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                29                379 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                47                361 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                47                361 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               116                292 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               116                292 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                91                317 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                91                317 
[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 
                57                351 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                57                351 
[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 
                75                333 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                75                333 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                82                326 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                82                326 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                56                352 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                56                352 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               135                273 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               135                273 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               116                292 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               116                292 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                61                347 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                61                347 
[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 
               132                276 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               132                276 
[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 
               230                178 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               230                178 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               116                292 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               116                292 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                48                360 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                48                360 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               65               343 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               65               343 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               45               363 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               45               363 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               31               377 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               31               377 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               31               377 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               31               377 
[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 
               92               316 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               92               316 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               51               357 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               51               357 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               385 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               385 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              144               264 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              144               264 
[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 
               54               354 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               54               354 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              160               248 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              160               248 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              103               305 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              103               305 
[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 
               20               388 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               20               388 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               28               380 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               28               380 
[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 
              174               234 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              174               234 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              169               239 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              169               239 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                73                335 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                73                335 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               129                279 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               129                279 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               178                230 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               178                230 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               129                279 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               129                279 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                54                354 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                54                354 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                58                350 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                58                350 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                85                323 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                85                323 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               121                287 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               121                287 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               144                264 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               144                264 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               110                298 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               110                298 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               107                301 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               107                301 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               182                226 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               182                226 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                46                362 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                46                362 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                98                310 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                98                310 
[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 
                95                313 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                95                313 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                59                349 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                59                349 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                32                376 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                32                376 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                15                393 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                15                393 
[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 
               160                248 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               160                248 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               73               335 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               73               335 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               83               325 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               83               325 
[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=214,	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 
236  47  75   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
236  47  75   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
236  47  75   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
236  47  75   8 
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    45  43
  1P GAIN WILD-TYPE 182 135
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               88               317 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               43               135 
$`1P GAIN MUTATED`
TCGA-BT-A20T TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A3IN TCGA-DK-A3IU 
       14.89        25.94         8.98        12.92         8.22        23.21 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA75 TCGA-DK-AA77 
       17.98        64.18        38.24       166.03        11.18        20.32 
TCGA-E7-A541 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS 
       25.58         4.01        60.66        24.30        19.79        12.85 
TCGA-FD-A5C0 TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-GC-A3BM 
       18.08         3.06         9.67        31.07        17.23        21.40 
TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-XF-A8HD 
       19.13        24.92        10.92        20.28        22.72        97.45 
TCGA-XF-A9T5 TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M 
       66.64        98.99        44.32        86.30        18.58        13.64 
TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BT-A20R 
        3.48        19.69        10.22        47.80         2.66         5.06 
TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CF-A3MI TCGA-CU-A5W6 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.16         1.94        12.16         1.84         7.79       142.78 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6U TCGA-E5-A4U1 TCGA-E7-A5KE 
       13.58         8.15        15.02        19.00        38.83         0.56 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A5BU TCGA-FT-A3EE 
        8.09         8.94         5.52        22.98        19.33         3.25 
TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GD-A3OS TCGA-GV-A3JV 
       20.12        29.36        15.81         0.49        20.98        14.27 
TCGA-HQ-A2OF TCGA-K4-A5RH TCGA-K4-A5RI TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       64.01         9.07        11.70        15.32        15.58        13.48 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A9SG 
       38.99        22.68         3.02        29.56         6.21        48.62 
TCGA-XF-A9SU TCGA-XF-AAMT TCGA-ZF-A9R7 TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4X 
        5.98         2.96        21.86        20.22        59.38        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        54.21        29.49 

$`1P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A9FL 
       26.14         8.35        20.48         9.96        28.70        18.58 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
        4.90        15.12        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS 
       16.70       130.88        46.68        87.32        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       21.30         9.67        66.05        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W 
       15.68        50.70        36.66        52.01       165.73        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       13.64        56.15        15.35         0.92         1.22        33.04 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43X 
       23.41        17.98        29.16        46.78        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
       12.36         4.31        11.08        33.01        17.62        70.32 
TCGA-GC-A3WC TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E 
       17.75        32.78        32.98        19.82        27.35         8.58 
TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       19.07         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A8HF 
        1.84        33.14        86.83        51.32       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       15.35         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-YC-A8S6 
       71.57        91.73        30.94        61.45         3.88         9.63 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 
       21.11        30.28        94.29        88.87        34.06        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         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-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM 
        0.62        41.75        51.16        66.54         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       12.16        17.88        19.50        14.96         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
       16.18         4.67        17.56        36.43        28.41        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-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       13.08         5.19        29.79        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK 
      112.44        16.14        17.62        15.62        17.95         4.80 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       20.81        10.55       163.30        13.58        18.81        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       12.03        43.59        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
       16.70         0.66        26.96        26.24         4.24        24.03 
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-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP 
       32.02        16.77        12.62        22.52        27.98        25.74 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       14.96        20.91         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
       66.02         6.94        20.71        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       13.91        26.70         2.10         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       38.60        12.16        21.24        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI 
       16.27        11.80        44.38         1.15        21.07        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P 
       16.67        16.54        17.62        37.05        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB 
       69.34       112.83        35.24        17.82         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        6.58         1.87        17.88        64.80        79.66        66.41 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW 
       23.64        28.24        16.27        92.98       110.60         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        6.77        56.48        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
       11.97        22.36        25.41        31.20        35.84        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U 
       13.41        64.08        58.72        47.84         2.89         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-GU-AATO 
       60.16        19.40         8.52         5.52        10.65 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.49              0.62 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           166.03            165.73 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            18.79             17.56 
[1] "0.5 - 166.0 (18.8)" "0.6 - 165.7 (17.6)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         0       25        27       37
  1P GAIN WILD-TYPE       2      104       113       98
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               25               104
  STAGE III              27               113
  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
  1P GAIN MUTATED         22  45  14
  1P GAIN WILD-TYPE      101 150  44
D1V4, multiclass
          clus
vv         1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1+T2              22               101
  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    42  16  18   3
  1P GAIN WILD-TYPE 194  31  57   5
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              42               194
  N1              16                31
  N2              18                57
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    42   1
  1P GAIN WILD-TYPE 150  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     42    1
  1P GAIN WILD-TYPE  150   10
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              42               150
  1               1                10
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    25  64
  1P GAIN WILD-TYPE  82 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     25   64
  1P GAIN WILD-TYPE   82  237
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              25                82
  MALE                64               237
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    79   3
  1P GAIN WILD-TYPE 285  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     79    3
  1P GAIN WILD-TYPE  285   17
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               79               285
  YES               3                17
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, continuous
D1V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       4                         5    74
  1P GAIN WILD-TYPE    39                        17   253
D1V12, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   4                39
  BLACK OR AFRICAN AMERICAN               5                17
  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"
D1V13, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2  82
  1P GAIN WILD-TYPE   7 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   82
  1P GAIN WILD-TYPE    7  287
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              82               287
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    68  57
  1Q GAIN WILD-TYPE 159 121
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              125               280 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               57               121 
$`1Q GAIN MUTATED`
TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN 
       14.89        20.48        28.70         8.98        18.58        12.92 
TCGA-CU-A3KJ TCGA-DK-A3IN TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-AA6L 
       18.48         8.22        17.98        64.18        67.36        38.24 
TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA77 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
      166.03        13.64        20.32         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5C0 
       23.41        17.98        19.79        12.85         3.62        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TG TCGA-FD-A6TI TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       58.92         3.06         9.67        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-KQ-A41N TCGA-XF-A8HD 
       24.92        10.92        22.72        25.02        52.73        97.45 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-AAMY 
       15.35         3.22        15.98        11.90        66.64        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-A9RE 
       44.32        86.30        18.58        13.64        94.29         3.48 
TCGA-2F-A9KP TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13J 
       11.97        41.75        51.16        10.22        47.80         2.66 
TCGA-BL-A3JM TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A3MI 
        6.74         5.06        17.16        28.41         1.94        12.16 
TCGA-CF-A47V TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AD 
       12.46        11.34        11.87         1.84        21.86       112.44 
TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
        7.79        13.58         8.15        15.02        18.81        19.00 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A5KF TCGA-E7-A7PW TCGA-E7-A97Q 
       38.83        29.72         5.36         0.66        13.68         8.09 
TCGA-FD-A3B5 TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A5BU TCGA-FJ-A3ZE TCGA-FT-A3EE 
        8.94         5.52        22.98        19.33        10.65         3.25 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS 
       29.36        15.81         0.49        26.70         2.10        20.98 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RH 
       14.27        19.10        36.49        38.60        64.01         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       11.70        17.72        44.38         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PB 
       13.48        12.23        38.99        22.68         3.02        29.56 
TCGA-UY-A9PE TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SU TCGA-XF-AAMT TCGA-XF-AAN0 
        6.21        17.88        48.62         5.98         2.96        56.48 
TCGA-YC-A9TC TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4X 
        0.66        21.86        13.41        20.22        59.38        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       56.35        35.41        54.21        29.49        10.65 

$`1Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CU-A0YO TCGA-CU-A0YR 
       26.14         8.35        25.94         9.96         4.90        15.12 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       87.32        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       66.05        53.29        76.60        15.68        50.70        36.66 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ 
       52.01       165.73        13.64        56.15        11.18        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3SN TCGA-FD-A3SQ 
       25.58         0.92         1.22        33.04        29.16        46.78 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        8.25         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
       12.36         4.31        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.62        70.32        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB 
       27.35         8.58        19.07         9.01         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
        9.14        27.68        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A8HF 
        1.84        33.14        86.83        51.32       125.49        97.12 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 
       34.45        14.93         4.21        12.76        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90         2.24         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 
       54.90         7.63        71.57        91.73        30.94        61.45 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA4R 
        3.88         9.63        21.11        30.28        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR 
       19.69        57.90        12.23        24.13        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       50.04         0.62        66.54         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        7.33         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
       19.50         5.06        14.96         8.25        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       17.56        36.43        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       12.59        12.13        13.08        10.95        12.66        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE 
       13.08         5.19        29.79        66.41        18.41        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3WW 
       17.62        15.62        17.95       142.78         4.80        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       10.55       163.30        13.58        15.35        12.03        43.59 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 
       22.16         2.24        16.70         0.56        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        4.24        24.03        24.66        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       14.37        32.02        16.77        12.62        22.52        27.98 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       25.74        14.96        20.91         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 
        7.10        13.35         2.27        10.85        12.66         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12        66.02         6.94        20.71        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        8.94        13.91         3.12         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW 
        7.63        20.05        15.78         4.73         7.00        21.34 
TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A6FZ 
        8.48         1.51        19.40        12.16        21.24         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 
       15.42        16.27        11.80        21.07        16.67        16.54 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD 
       17.62        37.05        76.01        78.25        69.34       112.83 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       35.24        17.82         3.85        45.04         6.58         1.87 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        79.66        66.41        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 
       92.98       110.60         8.32         6.77        27.06        75.39 
TCGA-YC-A89H TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       18.84        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U 
       28.41        64.08        58.72        47.84         2.89         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       60.16        19.40         8.52         5.52 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.49              0.56 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           166.03            165.73 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            17.98             17.49 
[1] "0.5 - 166.0 (18.0)" "0.6 - 165.7 (17.5)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         0       36        36       53
  1Q GAIN WILD-TYPE       2       93       104       82
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               36                93
  STAGE III              36               104
  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
  1Q GAIN MUTATED         34  62  19
  1Q GAIN WILD-TYPE       89 133  39
D2V4, multiclass
          clus
vv         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1+T2              34                89
  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    60  19  30   4
  1Q GAIN WILD-TYPE 176  28  45   4
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              60               176
  N1              19                28
  N2              30                45
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    57   5
  1Q GAIN WILD-TYPE 135   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     57    5
  1Q GAIN WILD-TYPE  135    6
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              57               135
  1               5                 6
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    33  93
  1Q GAIN WILD-TYPE  74 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     33   93
  1Q GAIN WILD-TYPE   74  208
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              33                74
  MALE                93               208
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   107   8
  1Q GAIN WILD-TYPE 257  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    107    8
  1Q GAIN WILD-TYPE  257   12
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              107               257
  YES               8                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   102
  1Q GAIN WILD-TYPE    34                        14   225
D2V12, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN               8                14
  WHITE                                 102               225
[1] 3 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     2 114
  1Q GAIN WILD-TYPE   7 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2  114
  1Q GAIN WILD-TYPE    7  255
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO             114               255
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    61  50
  2P GAIN WILD-TYPE 166 128
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              111               294 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               50               128 
$`2P GAIN MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ 
       16.77        15.12        12.39         8.35        20.48        25.94 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YR TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN 
       28.70         8.98        15.12       130.88        87.32         8.22 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       66.05        17.98        64.18        67.36        15.68        36.66 
TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E7-A541 TCGA-FD-A3NA 
       38.24       166.03        13.64        11.18        25.58        60.66 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
       46.78        19.79        27.35         6.15        12.36         3.06 
TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-GU-AATP TCGA-GV-A3QF 
        4.31        17.23        11.08        17.62        32.98        20.28 
TCGA-GV-A3QK TCGA-K4-A3WS TCGA-KQ-A41O TCGA-KQ-A41P TCGA-XF-A8HD TCGA-XF-A8HG 
       27.35        25.02        50.56        35.97        97.45        15.35 
TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-AAMZ TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA4T 
       15.98        14.93        44.32        94.29        34.06        19.69 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-5N-A9KM TCGA-BL-A13J TCGA-BT-A0YX 
        0.62        41.75        51.16        17.42         2.66        13.15 
TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS 
       19.04         5.06        16.18        28.41        23.01        12.56 
TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A8HY TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       12.13        12.62        11.34        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-AA6P 
      112.44        17.95         7.79         4.80         8.15        15.02 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A6ME TCGA-E7-A97Q 
       18.81        19.00        12.03        43.59        24.03         8.09 
TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TF TCGA-FT-A3EE TCGA-GC-A6I3 
       20.91        27.45         7.10         2.27         3.25        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3QH 
       26.70         2.10        20.98        20.05         7.00         8.48 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
       19.40        38.60        21.24        11.70         1.81        15.42 
TCGA-KQ-A41R TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB 
       44.38        17.62        22.68        69.34       112.83        29.56 
TCGA-UY-A9PE TCGA-XF-AAMG TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9RN TCGA-ZF-AA4V 
        6.21       110.60        22.36        31.20        20.22        59.38 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       56.35        19.40         8.52 

$`2P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A3PK 
      108.95        16.27        33.83        26.14        14.89         9.96 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       18.58        12.92         4.90        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       19.00        16.70        46.68        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6M 
       23.21         9.67        53.29        76.60        50.70        52.01 
TCGA-DK-AA6R TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU 
      165.73        13.64        56.15        20.32        15.35         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        1.22        33.04         4.01        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       29.16        12.85         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       10.78         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES 
       62.86        18.81        12.69         9.67        31.07        33.01 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       70.32        21.40        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       32.78        19.82         8.58        19.07        22.72         9.01 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q 
        3.45         2.76         9.14        27.68        52.73        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HE 
       14.24         1.84        33.14        86.83        51.32       125.49 
TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       97.12         3.22        34.45         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       91.73        98.99        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE 
        3.88         9.63        13.64        21.11        30.28         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       88.87        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       27.62        50.04        66.54        10.22        47.80         2.50 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P 
       40.08         7.33         6.74         6.58        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH 
       19.50         5.06        14.96         8.25        17.16         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF 
       17.56        36.43         1.94        12.79        13.97        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-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1AE TCGA-DK-A1AF 
       13.08         5.19        29.79         1.84        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       15.62       142.78        13.58        20.81        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       13.58        15.35        38.83        29.72         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        4.24        24.66        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU 
       27.98         5.52        25.74        22.98        14.96        19.33 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        5.36         2.70        13.35        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OQ 
       15.81        15.91        14.07         0.49         8.94         3.12 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 
        2.20        11.31        18.97         7.63        15.78         4.73 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF 
       14.27        21.34        19.10        36.49         1.51        64.01 
TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S 
       12.16         9.07        17.72        16.27        11.80         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.32        15.58        21.07        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       16.54        38.99        37.05        76.01        78.25         3.02 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       35.24        17.82         3.85        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW 
       23.64        28.24        16.27        92.98         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        6.77        56.48        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       11.97        25.41        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       64.08        58.72        47.84         2.89         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       67.20        35.41        54.21        29.49         5.52        10.65 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.62              0.49 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           166.03            165.73 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             19.4              16.7 
[1] "0.6 - 166.0 (19.4)" "0.5 - 165.7 (16.7)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED         0       30        32       48
  2P GAIN WILD-TYPE       2       99       108       87
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               30                99
  STAGE III              32               108
  STAGE IV               48                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  2P GAIN MUTATED         30  53  16
  2P GAIN WILD-TYPE       93 142  42
D3V4, multiclass
          clus
vv         2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1+T2              30                93
  T3                    53               142
  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
  2P GAIN MUTATED    51  16  29   3
  2P GAIN WILD-TYPE 185  31  46   5
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              51               185
  N1              16                31
  N2              29                46
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    50   5
  2P GAIN WILD-TYPE 142   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     50    5
  2P GAIN WILD-TYPE  142    6
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              50               142
  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  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     95    5
  2P GAIN WILD-TYPE  269   15
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               95               269
  YES               5                15
[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    30  25
  2Q GAIN WILD-TYPE 197 153
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               55               350 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               25               153 
$`2Q GAIN MUTATED`
TCGA-BL-A5ZZ TCGA-BT-A42C TCGA-CU-A0YR TCGA-DK-A3IN TCGA-DK-AA6L TCGA-DK-AA6W 
       12.39        28.70        15.12         8.22        38.24        13.64 
TCGA-DK-AA75 TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A6TG TCGA-FJ-A3ZF TCGA-G2-A3VY 
       11.18        60.66        46.78         3.06        17.23        17.62 
TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A40G TCGA-K4-A3WS TCGA-KQ-A41O TCGA-XF-A8HD 
       32.98        20.28        19.07        25.02        50.56        97.45 
TCGA-XF-A9SK TCGA-ZF-A9RC TCGA-ZF-AA4T TCGA-4Z-AA82 TCGA-5N-A9KM TCGA-BL-A13J 
       15.98        94.29        19.69        51.16        17.42         2.66 
TCGA-BT-A20J TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42F TCGA-CF-A3MG TCGA-CF-A8HY 
       19.04        16.18        17.56        28.41        12.13        11.34 
TCGA-CF-A9FF TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-AA6P 
       11.87        66.41       112.44        17.95         7.79        15.02 
TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-FD-A62O TCGA-GD-A3OS TCGA-GU-AATQ 
       19.00        12.03        43.59         7.10        20.98         7.00 
TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ 
        8.48        19.40        64.01        21.24        11.70         1.81 
TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PB TCGA-ZF-A9R0 TCGA-ZF-AA51 
       17.62        22.68       112.83        29.56        22.36        56.35 
TCGA-ZF-AA56 
        8.52 

$`2Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N 
      108.95        16.27        16.77        15.12        33.83        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ 
       14.89         8.35        20.48        25.94         9.96         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       18.58        12.92         4.90        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ 
       19.00        16.70       130.88        46.68        87.32        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        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-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA74 
       36.66        52.01       165.73       166.03        13.64        56.15 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SR 
        4.01        24.30        23.41        17.98        29.16        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       12.85        27.35         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       10.78         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
       62.86        18.81         6.15        12.69        12.36         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM 
        9.67        31.07        11.08        33.01        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ 
       19.13        17.75        24.92        10.92        32.78        19.82 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB 
       27.35         8.58        22.72         9.01         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
        9.14        27.68        52.73        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A8HF 
        1.84        33.14        86.83        51.32       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
       15.35         3.22        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P 
       30.28         3.48        88.87        34.06        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         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-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 
       41.75        66.54        10.22        47.80         2.50        40.08 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        7.33         6.74         6.58        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A3PH TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
        4.67        36.43         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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.34        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 
       21.86        18.41        16.14        17.62        15.62       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.58        18.81        15.35        38.83        29.72         5.36 
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-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.70        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       20.71        15.81        15.91        14.07         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       13.91        26.70         2.10         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV 
       18.97         7.63        20.05        15.78         4.73        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE 
       21.34        19.10        36.49         1.51        38.60        12.16 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
        9.07        17.72        15.42        16.27        11.80        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-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P 
       16.67        16.54        38.99        37.05        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34         3.02        35.24        17.82         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       45.04         6.58         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        11.97        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       60.16        67.20        35.41        19.40        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.81              0.49 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           112.83            166.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            19.00             17.16 
[1] "1.8 - 112.8 (19.0)" "0.5 - 166.0 (17.2)"
[1] "hr=" "1"  
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED         0       18        16       21
  2Q GAIN WILD-TYPE       2      111       124      114
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               18               111
  STAGE III              16               124
  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
  2Q GAIN MUTATED         17  21   7
  2Q GAIN WILD-TYPE      106 174  51
D4V4, multiclass
          clus
vv         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1+T2              17               106
  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
  2Q GAIN MUTATED    29   8  11   1
  2Q GAIN WILD-TYPE 207  39  64   7
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              29               207
  N1               8                39
  N2              11                64
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    23   1
  2Q GAIN WILD-TYPE 169  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     23    1
  2Q GAIN WILD-TYPE  169   10
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              23               169
  1               1                10
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    18  37
  2Q GAIN WILD-TYPE  89 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     18   37
  2Q GAIN WILD-TYPE   89  264
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              18                89
  MALE                37               264
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    51   1
  2Q GAIN WILD-TYPE 313  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     51    1
  2Q GAIN WILD-TYPE  313   19
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               51               313
  YES               1                19
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, continuous
D4V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       5                         3    45
  2Q GAIN WILD-TYPE    38                        19   282
D4V12, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   5                38
  BLACK OR AFRICAN AMERICAN               3                19
  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"
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    75  66
  3P GAIN WILD-TYPE 152 112
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              141               264 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               66               112 
$`3P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20W TCGA-BT-A2LD 
       16.27        16.77        15.12        12.39         8.35        20.48 
TCGA-BT-A3PK TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A2I6 
        9.96         4.90        15.12         2.14        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B6 
        8.22        50.27        23.21        17.98        64.18        36.66 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-E5-A4TZ TCGA-FD-A43P TCGA-FD-A5C0 
      166.03        13.64        13.64        15.35        27.35        18.08 
TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF 
        6.28        12.36         3.06         4.31         9.67        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GU-A42P TCGA-GV-A3QF TCGA-GV-A3QK 
       11.08        33.01        17.62        10.92        20.28        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-KQ-A41O 
       19.07        22.72         9.01        25.02         3.45        50.56 
TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       35.97        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SV TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAML 
       97.12        15.35        12.76        13.74        10.82         7.63 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4T TCGA-ZF-AA53 
       98.99        44.32        30.28        94.29        19.69        57.90 
TCGA-2F-A9KO TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A13I 
       24.13        34.98        27.62        47.80        17.42         7.33 
TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A3PH TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG 
        2.66        19.04         4.67        12.79        12.59        12.13 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-AA6U 
       29.79         1.84        21.86       112.44        17.95        19.00 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A5KE TCGA-E7-A6MD 
       12.03        43.59        38.83         5.36         0.56         4.24 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A43U TCGA-FD-A62O TCGA-FD-A6TF 
       24.03        13.68         8.09        20.91         7.10         2.27 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-AA3F 
       10.65         3.25        61.94        48.00        59.31        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A762 
       20.71        15.81         0.49         2.10        20.98         7.63 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE 
        7.00        14.27        21.34         8.48        19.40        38.60 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
       21.24         9.07        15.42        11.80        44.38         1.15 
TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OC 
       12.23        38.99        17.62        37.05        69.34         3.02 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       29.56        17.82         6.58         1.87        17.88        48.62 
TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAMX TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       79.66         5.98         6.77        22.36        13.41        64.08 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       47.84         2.89        59.38        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-GU-AATO 
       19.40        54.21        10.65 

$`3P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A3PJ TCGA-BT-A42C 
      108.95        33.83        26.14        14.89        25.94        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA 
        8.98        18.58        12.92        18.48        13.58        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 
       16.70       130.88        17.72        21.30         9.67        66.05 
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-AA6R TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 
       52.01       165.73        56.15        11.18        20.32        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        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-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
        3.62        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        8.25        58.92        62.86        18.81         6.15        12.69 
TCGA-FJ-A3Z7 TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       31.07        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A40E TCGA-K4-A4AB TCGA-K4-A4AC 
       32.78        32.98        19.82         8.58         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SJ 
       27.68        52.73        46.98        97.45       125.49         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY 
       15.98        34.45        14.93         4.21        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMH 
       26.27        18.90         2.24        66.64         2.10        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       54.90        71.57        91.73        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE 
       18.58         3.88         9.63        13.64        21.11         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       88.87        34.06        12.23        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA80 
        8.35        44.94        16.83        17.16        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A0C8 
       41.75        51.16        66.54        10.22         2.50        40.08 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS 
       17.56        36.43        28.41         1.94        23.01        12.56 
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-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-DK-A1A6 
       11.34        11.34        11.87        13.08         5.19        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.41        16.14        17.62        15.62         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E7-A3X6 TCGA-E7-A4IJ 
       15.02        13.58        18.81        15.35        29.72        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        2.24        16.70         0.66        26.96        26.24        24.66 
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-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       22.98        14.96        19.33         5.36        27.45         2.70 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EK TCGA-G2-A2EL 
       13.35        10.85        12.66         8.94        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3RC TCGA-GC-A3RD 
        7.23        20.12        66.02         6.94        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
        8.94        13.91        26.70         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QI 
       18.97        20.05        15.78         4.73        19.10        36.49 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        1.51        64.01        12.16        11.70        17.72         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
       16.27        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        35.24 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX 
        6.21         3.85        45.04        64.80        66.41        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RG 
       25.41        31.20        35.84        21.86        28.41        58.72 
TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       20.22         8.61        60.16         8.52        29.49         5.52 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.49              0.62 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           166.03            165.73 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            17.82             17.59 
[1] "0.5 - 166.0 (17.8)" "0.6 - 165.7 (17.6)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         0       46        39       57
  3P GAIN WILD-TYPE       2       83       101       78
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               46                83
  STAGE III              39               101
  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         41  60  27
  3P GAIN WILD-TYPE       82 135  31
D5V4, multiclass
          clus
vv         3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1+T2              41                82
  T3                    60               135
  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
  3P GAIN MUTATED    67  18  35   4
  3P GAIN WILD-TYPE 169  29  40   4
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              67               169
  N1              18                29
  N2              35                40
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    63   6
  3P GAIN WILD-TYPE 129   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     63    6
  3P GAIN WILD-TYPE  129    5
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              63               129
  1               6                 5
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    31 112
  3P GAIN WILD-TYPE  76 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     31  112
  3P GAIN WILD-TYPE   76  189
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              31                76
  MALE               112               189
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED   124   8
  3P GAIN WILD-TYPE 240  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    124    8
  3P GAIN WILD-TYPE  240   12
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO              124               240
  YES               8                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   123
  3P GAIN WILD-TYPE    33                        17   204
D5V12, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                  10                33
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                 123               204
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     3 129
  3P GAIN WILD-TYPE   6 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3  129
  3P GAIN WILD-TYPE    6  240
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             129               240
[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 131  97
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              177               228 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               81                97 
$`3Q GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20W TCGA-BT-A2LD 
       16.27        16.77        15.12        12.39         8.35        20.48 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1AC 
        9.96        28.70         4.90        15.12        18.48       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 
       46.68        87.32         8.22        50.27        23.21        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S 
       64.18        15.68        36.66        38.24       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B6 
       13.64        13.64        20.32        15.35        25.58        33.04 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TC 
       24.30        23.41        27.35        18.08         6.28         6.15 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P 
       12.36         3.06         4.31         9.67        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3WC TCGA-GU-A42P TCGA-GV-A3QF TCGA-GV-A3QK 
       33.01        17.62        17.75        10.92        20.28        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-KQ-A41O 
       19.07        22.72         9.01        25.02         3.45        50.56 
TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       35.97        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9T5 TCGA-XF-A9T8 
       97.12        15.35         3.22        12.76        66.64        13.74 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3M 
        7.63        71.57        98.99        44.32        86.30        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-ZF-AA53 
       21.11        30.28        94.29         3.48        19.69        57.90 
TCGA-2F-A9KO TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 
       24.13        34.98        27.62        47.80        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20X 
        7.33         2.66        13.15        19.04         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF 
       17.16         4.67        36.43        12.79        12.56        12.59 
TCGA-CF-A3MG TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       12.13        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC 
      112.44        17.95         4.80        19.00        12.03        43.59 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW 
        5.36        22.16         0.56         4.24        24.03        13.68 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3N5 TCGA-FD-A43U TCGA-FD-A62O 
       12.95         8.09        32.02        22.52        20.91         7.10 
TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-AA3F 
        2.27        10.65        61.94        48.00        59.31        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        14.07         0.49         8.94        13.91 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A762 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10        20.98         7.63         7.00        14.27        21.34 
TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6MB 
        8.48        19.40        38.60        21.24         9.07        15.42 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78K 
       11.80        44.38         1.15        12.23        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HB 
       37.05        69.34         3.02        29.56        17.82        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SZ 
        6.58         1.87        17.88        79.66         5.98        28.24 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM 
        2.96         6.77        22.36        13.41        64.08        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       20.22         2.89        59.38        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-GU-AATO 
       19.40        54.21        10.65 

$`3Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A3PJ TCGA-C4-A0EZ 
      108.95        33.83        26.14        14.89        25.94         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       18.58        12.92        13.58         2.14        19.00        16.70 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
       17.72        21.30         9.67        66.05        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E7-A7DU 
       67.36        50.70        52.01        56.15        11.18         0.92 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        1.22         4.01        60.66        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        12.85         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB 
       10.78         5.69         8.25        58.92        62.86        18.81 
TCGA-FD-A6TD TCGA-FJ-A3Z7 TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS 
       12.69        31.07        70.32        21.40        19.13        24.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A40E TCGA-K4-A4AB TCGA-K4-A4AC 
       32.78        32.98        19.82         8.58         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SK 
       27.68        52.73        46.98        97.45       125.49        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       34.45        14.93         4.21        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       18.90         2.24         2.10        10.82        11.31        54.90 
TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       91.73        30.94        61.45        18.58         3.88         9.63 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       88.87        34.06        12.23        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA80 
        8.35        44.94        16.83        17.16        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A3JM 
       41.75        51.16        66.54        10.22         2.50         6.74 
TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
        6.58        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C 
       16.18        17.56        28.41         1.94        23.01        13.97 
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-A9FM TCGA-CU-A3QU TCGA-DK-A1AE TCGA-DK-A1AF 
       11.34        11.87        13.08         5.19        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
       15.62         7.79       142.78        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       10.55       163.30        15.02        13.58        18.81        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       38.83        29.72         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 
       26.24        24.66        14.07        15.32        14.37        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
        8.94        12.62        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S 
       14.96        19.33         5.36        27.45         2.70        13.35 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL 
       10.85        12.66         8.94         3.25        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3RC TCGA-GD-A2C5 
        7.23        20.12        66.02         6.94        15.91        26.70 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 
        3.12         2.20        11.31        18.97        20.05        15.78 
TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE 
        4.73        19.10        36.49         1.51        64.01        12.16 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
       11.70        17.72         1.81        16.27        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-A9SG 
       78.25       112.83        35.24         6.21         3.85        48.62 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
       64.80        66.41        23.64        16.27        92.98       110.60 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        8.32        56.48        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       11.97        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RG TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       58.72         8.61        60.16         8.52        29.49         5.52 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.49              0.62 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           166.03            163.30 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            18.08             16.70 
[1] "0.5 - 166.0 (18.1)" "0.6 - 163.3 (16.7)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         1       55        50       72
  3Q GAIN WILD-TYPE       1       74        90       63
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               55                74
  STAGE III              50                90
  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
  3Q GAIN MUTATED         51  81  30
  3Q GAIN WILD-TYPE       72 114  28
D6V4, multiclass
          clus
vv         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1+T2              51                72
  T3                    81               114
  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
  3Q GAIN MUTATED    83  24  44   4
  3Q GAIN WILD-TYPE 153  23  31   4
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              83               153
  N1              24                23
  N2              44                31
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    82   7
  3Q GAIN WILD-TYPE 110   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     82    7
  3Q GAIN WILD-TYPE  110    4
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              82               110
  1               7                 4
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    46 133
  3Q GAIN WILD-TYPE  61 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     46  133
  3Q GAIN WILD-TYPE   61  168
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              46                61
  MALE               133               168
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   159   9
  3Q GAIN WILD-TYPE 205  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    159    9
  3Q GAIN WILD-TYPE  205   11
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO              159               205
  YES               9                11
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, continuous
D6V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED      13                         8   153
  3Q GAIN WILD-TYPE    30                        14   174
D6V12, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                  13                30
  BLACK OR AFRICAN AMERICAN               8                14
  WHITE                                 153               174
[1] 3 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     4 162
  3Q GAIN WILD-TYPE   5 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4  162
  3Q GAIN WILD-TYPE    5  207
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             162               207
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    28   9
  4P GAIN WILD-TYPE 199 169
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               37               368 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               169 
$`4P GAIN MUTATED`
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 
       18.48         2.14       130.88        66.05        64.18        67.36 
TCGA-DK-AA75 TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3NA TCGA-FD-A6TC TCGA-FD-A6TE 
       11.18        25.58         0.92        60.66         6.15        12.36 
TCGA-GU-A42P TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-UY-A78N TCGA-XF-A9T3 TCGA-ZF-A9R2 
       10.92        22.72         9.01        86.83         2.24        21.11 
TCGA-4Z-AA87 TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF 
       47.80        23.01        12.62        12.00        11.34        11.87 
TCGA-DK-A1A6 TCGA-DK-A2I2 TCGA-E5-A4U1 TCGA-E7-A6MD TCGA-FD-A5BV TCGA-FD-A5BZ 
       66.41         7.79        38.83         4.24         5.36        27.45 
TCGA-G2-A2EF TCGA-K4-A6FZ TCGA-KQ-A41R TCGA-MV-A51V TCGA-UY-A78O TCGA-YF-AA3L 
       61.94         1.81        44.38        13.48        76.01        11.97 
TCGA-ZF-AA5H 
       29.49 

$`4P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       28.70         8.98        18.58        12.92         4.90        15.12 
TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       13.58        19.00        16.70        46.68        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 
       17.72        50.27        21.30        23.21         9.67        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       53.29        76.60        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ 
       20.32        15.35         1.22        33.04         4.01        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-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35         3.62        15.58        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
        5.69         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       18.81        12.69         3.06         4.31         9.67        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       17.23        11.08        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       19.13        17.75        24.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-K4-A3WS TCGA-K4-A3WU 
       20.28        27.35         8.58        19.07        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD 
       46.98        14.24         1.84        33.14        51.32        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
      125.49        97.12        15.35         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       13.64        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        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-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22         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-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        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-A47Y 
       12.16        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       13.12        12.10        11.34        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
        1.84        21.86        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62        17.95       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        12.03        43.59        29.72         5.36 
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-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       26.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       14.96        20.91        19.33         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
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        26.70         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-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
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-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       21.07        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        22.68        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 
       35.24        29.56        17.82         6.21         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        6.58         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39        18.84         0.66        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.92              0.49 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           130.88            166.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            18.48             17.62 
[1] "0.9 - 130.9 (18.5)" "0.5 - 166.0 (17.6)"
[1] "hr=" "2"  
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         18  16   3
  4P GAIN WILD-TYPE      105 179  55
D7V4, multiclass
          clus
vv         4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1+T2              18               105
  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 208  41  72   7
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              28               208
  N1               6                41
  N2               3                72
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    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    34   1
  4P GAIN WILD-TYPE 330  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     34    1
  4P GAIN WILD-TYPE  330   19
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               34               330
  YES               1                19
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, continuous
D7V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       5                         1    28
  4P GAIN WILD-TYPE    38                        21   299
D7V12, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   5                38
  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"
D7V13, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  32
  4P GAIN WILD-TYPE   8 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   32
  4P GAIN WILD-TYPE    8  337
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              32               337
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    19   6
  4Q GAIN WILD-TYPE 208 172
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               25               380 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               172 
$`4Q GAIN MUTATED`
TCGA-4Z-AA7M TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-FD-A3NA 
       16.27        18.48         2.14        66.05        67.36        60.66 
TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-GU-A42P TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-XF-AAN7 
       18.08        12.36        10.92        22.72         9.01        18.58 
TCGA-ZF-A9R2 TCGA-4Z-AA7W TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CF-A8HY TCGA-CF-A9FF 
       21.11        27.62        23.01        12.62        11.34        11.87 
TCGA-E5-A4U1 TCGA-FD-A5BV TCGA-G2-A2EF TCGA-UY-A78O TCGA-YF-AA3L TCGA-ZF-AA4W 
       38.83         5.36        61.94        76.01        11.97        60.16 
TCGA-ZF-AA5H 
       29.49 

$`4Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E 
        8.98        18.58        12.92         4.90        15.12        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       19.00        16.70       130.88        46.68        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 
       17.72        50.27        21.30        23.21         9.67        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-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       56.15        11.18        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        1.22        33.04         4.01        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       24.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
        8.58        19.07        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
        1.84        33.14        86.83        51.32        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       30.94        61.45        86.30         3.88         9.63        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
        8.35        44.94        16.83        17.16        34.98        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
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-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-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR 
        4.67        17.56        36.43        28.41         1.94        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.00        12.10        11.34        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
       13.58         8.15        20.81        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        18.81        19.00        15.35        12.03        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         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-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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        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-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        59.31         7.23        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW 
       29.36        20.71        15.81        15.91        14.07         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       21.07        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       17.62        37.05        22.68        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        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       45.04         6.58         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             2.14              0.49 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            76.01            166.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            18.58             17.59 
[1] "2.1 - 76.0 (18.6)"  "0.5 - 166.0 (17.6)"
[1] "hr=" "2.1"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         0       14         6        6
  4Q GAIN WILD-TYPE       2      115       134      129
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               14               115
  STAGE III               6               134
  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  12   0
  4Q GAIN WILD-TYPE      110 183  58
D8V4, multiclass
          clus
vv         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1+T2              13               110
  T3                    12               183
  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    20   3   3   0
  4Q GAIN WILD-TYPE 216  44  72   8
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              20               216
  N1               3                44
  N2               3                72
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    16   0
  4Q GAIN WILD-TYPE 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     7  19
  4Q GAIN WILD-TYPE 100 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7   19
  4Q GAIN WILD-TYPE  100  282
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               7               100
  MALE                19               282
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    24   1
  4Q GAIN WILD-TYPE 340  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     24    1
  4Q GAIN WILD-TYPE  340   19
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               24               340
  YES               1                19
[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  73
  5P GAIN WILD-TYPE 135 105
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              165               240 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               73               105 
$`5P GAIN MUTATED`
TCGA-2F-A9KT TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ 
      108.95        12.39        26.14        14.89         8.35        25.94 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A2I6 
        9.96        28.70        12.92        15.12        18.48        87.32 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 
        8.22        23.21         9.67        67.36        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SR 
       56.15        15.35        25.58         1.22        60.66        19.79 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB 
       15.58        26.73         8.25        58.92         6.28        18.81 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P 
        6.15        12.36         3.06         4.31        17.23        11.08 
TCGA-G2-AA3D TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G 
       70.32        24.92        10.92        20.28         8.58        19.07 
TCGA-K4-A4AC TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A8HF 
        9.14        50.56        46.98         1.84        86.83        97.12 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9T3 TCGA-XF-A9T5 
        3.22        15.98        34.45        14.93         2.24        66.64 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       54.90         7.63        18.58        13.64        30.28        94.29 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       88.87        34.06        19.69        57.90        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A3JM 
        0.62        41.75        10.22         2.50        40.08         6.74 
TCGA-BT-A20V TCGA-BT-A2LA TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
        5.06        17.16        12.56        12.59        12.13        13.08 
TCGA-CF-A47S TCGA-CF-A5UA TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A2I4 TCGA-DK-A3WX 
       10.95        12.00         5.19        21.86       142.78        10.55 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 
       15.02        13.58        19.00        15.35        38.83        29.72 
TCGA-E7-A4IJ TCGA-E7-A6MD TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       22.16         4.24        12.95         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A5BU TCGA-FD-A5BV 
        8.94        22.52         5.52        25.74        19.33         5.36 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FT-A3EE TCGA-G2-A2EO 
        2.70         7.10        13.35        10.85         3.25        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.23        20.12        66.02        29.36        20.71        15.81 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A766 TCGA-GU-AATQ 
        0.49        13.91         2.10        20.98        15.78         7.00 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A5NE 
       14.27        19.10         8.48        36.49        19.40        12.16 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
        9.07        11.70         1.81        44.38         1.15        15.32 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A8OB 
       13.48        16.67        38.99        17.62        37.05        69.34 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-AAME TCGA-XF-AAMT TCGA-ZF-A9R3 
       29.56         6.21        48.62        92.98         2.96        31.20 
TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       21.86        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       59.38        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       54.21        29.49        10.65 

$`5P GAIN WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A2LD TCGA-C4-A0EZ 
       16.27        16.77        15.12        33.83        20.48         8.98 
TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       18.58         4.90        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 
      130.88        46.68        17.72        50.27        21.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-AA75 
       17.98        64.18        53.29        76.60        15.68        11.18 
TCGA-DK-AA77 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL 
       20.32         0.92        33.04         4.01        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       17.98        29.16        46.78        12.85        27.35         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TD 
       53.88        10.78         5.69        18.08        62.86        12.69 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB 
        9.67        31.07        33.01        17.62        21.40        19.13 
TCGA-GC-A3WC TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A6ZA 
       17.75        32.78        32.98        19.82        27.35        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N 
        9.01        25.02         3.45         2.76        27.68        52.73 
TCGA-KQ-A41P TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
       35.97        14.24        33.14        51.32        97.45       125.49 
TCGA-XF-A8HG TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       15.35         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMQ 
       18.90         2.10        13.74        10.82        11.31        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-AA5P TCGA-2F-A9KO 
        3.88         9.63        21.11         3.48        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KM 
       17.16        34.98        51.16        66.54        47.80        17.42 
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-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        17.56        36.43        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.79        13.97        12.16        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.62        12.26        13.12        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 
       11.87        13.08        29.79         1.84        66.41        18.41 
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-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6T 
        4.80        13.58         8.15        20.81       163.30        18.81 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       12.03        43.59         5.36         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
        0.66        26.96        26.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A43N 
       14.07        15.32        14.37        12.62        27.98        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       14.96        20.91        27.45         2.27        12.66        10.65 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-AA3C 
        8.94        61.94        48.00        15.95        26.93         6.94 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 
       15.91        14.07         8.94        26.70         3.12         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A767 TCGA-GV-A3JW 
       11.31        18.97         7.63        20.05         4.73        21.34 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6MB 
        1.51        38.60        64.01        21.24        17.72        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 
       16.27        11.80        15.58        21.07        12.23        16.54 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       22.68        76.01        78.25         3.02       112.83        35.24 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI 
       17.82         3.85        45.04         6.58         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
       16.27       110.60         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       75.39        18.84         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA5N 
       35.84        28.41        13.41         8.61        60.16         5.52 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.49              0.56 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           166.03            163.30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            17.62             17.67 
[1] "0.5 - 166.0 (17.6)" "0.6 - 163.3 (17.7)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         1       57        57       51
  5P GAIN WILD-TYPE       1       72        83       84
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               57                72
  STAGE III              57                83
  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
  5P GAIN MUTATED         50  75  23
  5P GAIN WILD-TYPE       73 120  35
D9V4, multiclass
          clus
vv         5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1+T2              50                73
  T3                    75               120
  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
  5P GAIN MUTATED    90  23  25   2
  5P GAIN WILD-TYPE 146  24  50   6
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              90               146
  N1              23                24
  N2              25                50
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    73   1
  5P GAIN WILD-TYPE 119  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     73    1
  5P GAIN WILD-TYPE  119   10
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              73               119
  1               1                10
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    41 125
  5P GAIN WILD-TYPE  66 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     41  125
  5P GAIN WILD-TYPE   66  176
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              41                66
  MALE               125               176
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   148   8
  5P GAIN WILD-TYPE 216  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    148    8
  5P GAIN WILD-TYPE  216   12
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              148               216
  YES               8                12
[1] 2 2
[1] FALSE
D9V9, continuous
D9V10, continuous
D9V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED      10                        10   140
  5P GAIN WILD-TYPE    33                        12   187
D9V12, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                  10                33
  BLACK OR AFRICAN AMERICAN              10                12
  WHITE                                 140               187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    29  21
  5Q GAIN WILD-TYPE 198 157
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               50               355 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               21               157 
$`5Q GAIN MUTATED`
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A42C TCGA-DK-A2I6 TCGA-DK-A6B6 TCGA-DK-AA6L 
       26.14        14.89        28.70        87.32        36.66        38.24 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E7-A541 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TE 
       13.64        56.15        25.58        58.92         6.28        12.36 
TCGA-FD-A6TH TCGA-GC-A3YS TCGA-GV-A40E TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A9T5 
        4.31        24.92         8.58         1.84        86.83        66.64 
TCGA-XF-AAMZ TCGA-ZF-AA53 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-CF-A1HS 
       44.32        57.90         2.50        40.08         6.74        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-DK-A2I4 TCGA-DK-A3WX TCGA-E7-A85H TCGA-FD-A5BU 
       12.59        12.13       142.78        10.55        12.95        19.33 
TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GV-A3JV 
        3.25        59.31        29.36        20.71        15.81        14.27 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41S 
        8.48        36.49         9.07        11.70         1.81         1.15 
TCGA-LC-A66R TCGA-MV-A51V TCGA-UY-A78L TCGA-UY-A9PE TCGA-XF-A9SG TCGA-ZF-AA54 
       15.32        13.48        37.05         6.21        48.62        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 
        8.52        54.21 

$`5Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL 
        8.35        20.48        25.94         9.96         8.98        18.58 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       12.92         4.90        15.12        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ 
       19.00        16.70       130.88        46.68         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        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-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 
       52.01       165.73       166.03        13.64        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       15.35         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       12.85        27.35         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB 
       10.78         5.69         8.25        18.08        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.15        12.69         3.06         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.75        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       27.35        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
       46.98        14.24        33.14        51.32        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
        7.63        71.57        91.73        98.99        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         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-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       17.42         7.33         2.66         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-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MH 
       28.41         1.94        23.01        12.79        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
       17.95         7.79         4.80        13.58         8.15        20.81 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
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         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
        4.24        24.03        24.66        13.68        14.07        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       20.91         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EF 
        2.27        10.85        12.66        10.65         8.94        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       48.00        15.95        26.93         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
        6.94        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-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       21.34        19.10         1.51        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       12.16        21.24        17.72        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       44.38        15.58        21.07        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       38.99        17.62        22.68        76.01        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
        3.02       112.83        35.24        29.56        17.82         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       45.04         6.58         1.87        17.88        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       75.39        18.84         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       60.16        67.20        56.35        35.41        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.15              0.49 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           142.78            166.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           15.565            17.720 
[1] "1.1 - 142.8 (15.6)" "0.5 - 166.0 (17.7)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         1       13        21       16
  5Q GAIN WILD-TYPE       1      116       119      119
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               13               116
  STAGE III              21               119
  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
  5Q GAIN MUTATED         13  27   6
  5Q GAIN WILD-TYPE      110 168  52
D10V4, multiclass
          clus
vv         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1+T2              13               110
  T3                    27               168
  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
  5Q GAIN MUTATED    27   9   7   0
  5Q GAIN WILD-TYPE 209  38  68   8
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              27               209
  N1               9                38
  N2               7                68
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    19   0
  5Q GAIN WILD-TYPE 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  37
  5Q GAIN WILD-TYPE  93 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     14   37
  5Q GAIN WILD-TYPE   93  264
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              14                93
  MALE                37               264
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    48   1
  5Q GAIN WILD-TYPE 316  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     48    1
  5Q GAIN WILD-TYPE  316   19
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               48               316
  YES               1                19
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, continuous
D10V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       4                         1    44
  5Q GAIN WILD-TYPE    39                        21   283
D10V12, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   4                39
  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  48
  5Q GAIN WILD-TYPE   8 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   48
  5Q GAIN WILD-TYPE    8  321
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              48               321
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    40  33
  6P GAIN WILD-TYPE 187 145
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               73               332 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               33               145 
$`6P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A6B1 TCGA-DK-A6B2 
       16.27        16.77       130.88        87.32        67.36        15.68 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E7-A541 TCGA-FD-A3B7 TCGA-FD-A3SR TCGA-FD-A3SS 
       56.15        11.18        25.58         4.01        19.79        12.85 
TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FT-A61P TCGA-GC-A3BM TCGA-GC-A3YS 
       58.92         6.15         3.06        11.08        21.40        24.92 
TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A6ZA TCGA-K4-A4AC TCGA-SY-A9G0 TCGA-UY-A78N 
       10.92        32.98        22.72         9.14        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A9ST TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMQ 
       51.32        97.45         4.21        66.64         7.63        71.57 
TCGA-ZF-A9R4 TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-4Z-AA81 TCGA-BL-A0C8 TCGA-BT-A0S7 
       30.28        34.06        19.69        41.75        40.08         6.58 
TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5UA TCGA-DK-A3IM TCGA-DK-A3WX TCGA-FD-A6TF 
       12.46        12.62        12.00         8.15        10.55         2.27 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       10.65         3.25        66.02        20.71        15.81        15.91 
TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GU-A42R TCGA-GU-A762 TCGA-HQ-A5NE TCGA-K4-A5RH 
        0.49        26.70        18.97         7.63        12.16         9.07 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       11.80        15.32        15.58        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC 
       69.34         3.02        29.56         6.21         3.85         6.58 
TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA58 
       58.72        20.22        59.38        67.20        19.40        54.21 
TCGA-GU-AATO 
       10.65 

$`6P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        15.12        33.83        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        20.48        25.94         9.96        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
       18.58        12.92         4.90        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ 
        2.14        19.00        16.70        46.68         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA77 
       52.01       165.73       166.03        13.64        13.64        20.32 
TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       15.35         0.92         1.22        33.04        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43X 
       23.41        17.98        29.16        46.78        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
       18.08         6.28        62.86        18.81        12.69        12.36 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY 
        4.31         9.67        31.07        17.23        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF 
       70.32        19.13        17.75        32.78        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       27.35         8.58        19.07         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        2.76        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       14.24         1.84       125.49        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       15.98        34.45        14.93        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       26.27        18.90         2.24         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       11.31        54.90        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-ZF-AA5P 
       21.11        94.29         3.48        88.87        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         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-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
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-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY 
        7.79       142.78         4.80        13.58        20.81       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       24.03        24.66        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-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ 
       13.35        10.85        12.66         8.94        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       15.95        26.93        59.31         7.23        20.12         6.94 
TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ 
       29.36        14.07         8.94        13.91         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       20.98         2.20        11.31        20.05        15.78         4.73 
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-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI 
        1.51        19.40        38.60        64.01        21.24        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R TCGA-KQ-A41S 
       17.72         1.81        15.42        16.27        44.38         1.15 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       21.07        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-XF-A8HB 
       17.62        78.25       112.83        35.24        17.82        45.04 
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-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       18.84         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM 
       35.84        21.86        28.41        13.41        64.08        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 
        2.89         8.61        60.16        56.35        35.41         8.52 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       29.49         5.52 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.49              0.56 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           130.88            166.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            18.97             17.62 
[1] "0.5 - 130.9 (19.0)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1"  
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         1       19        24       29
  6P GAIN WILD-TYPE       1      110       116      106
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               19               110
  STAGE III              24               116
  STAGE IV               29               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  6P GAIN MUTATED         24  34  12
  6P GAIN WILD-TYPE       99 161  46
D11V4, multiclass
          clus
vv         6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1+T2              24                99
  T3                    34               161
  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
  6P GAIN MUTATED    37  11  16   2
  6P GAIN WILD-TYPE 199  36  59   6
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              37               199
  N1              11                36
  N2              16                59
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    28   2
  6P GAIN WILD-TYPE 164   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     28    2
  6P GAIN WILD-TYPE  164    9
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              28               164
  1               2                 9
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    14  59
  6P GAIN WILD-TYPE  93 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     14   59
  6P GAIN WILD-TYPE   93  242
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              14                93
  MALE                59               242
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    60   5
  6P GAIN WILD-TYPE 304  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     60    5
  6P GAIN WILD-TYPE  304   15
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               60               304
  YES               5                15
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, continuous
D11V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       5                         1    66
  6P GAIN WILD-TYPE    38                        21   261
D11V12, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   5                38
  BLACK OR AFRICAN AMERICAN               1                21
  WHITE                                  66               261
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     1  67
  6P GAIN WILD-TYPE   8 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   67
  6P GAIN WILD-TYPE    8  302
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              67               302
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    23  16
  6Q GAIN WILD-TYPE 204 162
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               39               366 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16               162 
$`6Q GAIN MUTATED`
TCGA-4Z-AA7Q TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A6B1 TCGA-DK-AA75 TCGA-FD-A3SS 
       16.77       130.88        87.32        67.36        11.18        12.85 
TCGA-FD-A5C1 TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GU-A42P TCGA-K4-A4AC TCGA-UY-A78N 
       58.92        21.40        24.92        10.92         9.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A9T5 TCGA-XF-AAMQ TCGA-ZF-A9R4 TCGA-ZF-AA4T 
       51.32        97.45        66.64        71.57        30.28        19.69 
TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A2LA TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5UA 
       40.08         6.58        17.16        12.46        12.62        12.00 
TCGA-DK-A3IM TCGA-DK-A3WX TCGA-FJ-A3ZE TCGA-GC-A3OO TCGA-K4-A5RH TCGA-K4-AAQO 
        8.15        10.55        10.65        15.81         9.07        11.80 
TCGA-LC-A66R TCGA-UY-A78L TCGA-XF-A8HC TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4V 
       15.32        37.05         6.58        58.72        20.22        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-GU-AATO 
       67.20        19.40        10.65 

$`6Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IN 
       13.58         2.14        19.00        16.70        46.68         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
       17.72        50.27        21.30        23.21         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       36.66        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       13.64        56.15        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X 
       17.98        29.16        46.78        19.79        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
       11.08        33.01        17.62        70.32        19.13        17.75 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
        1.84        33.14       125.49        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 
       21.04        26.27        18.90         2.24         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMY 
       10.82        11.31        54.90         7.63        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
        9.63        13.64        21.11        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       34.06        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        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-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80         2.50        17.42         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
        5.06        14.96         5.06         8.25        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        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-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 
       10.95        12.66        12.10        12.26        13.12        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        11.34        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       13.58        20.81       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        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-A7PW 
       26.96        26.24         4.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       12.66         8.94         3.25        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        59.31         7.23        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       29.36        20.71        15.91        14.07         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
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-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R 
       11.70        17.72         1.81        15.42        16.27        44.38 
TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.58        21.07        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
       16.54        38.99        17.62        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        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        6.21         3.85        45.04         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       13.41        64.08        47.84         2.89         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       56.35        35.41         8.52        54.21        29.49         5.52 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             6.58              0.49 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           130.88            166.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            19.40             17.62 
[1] "6.6 - 130.9 (19.4)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         1       11        15       12
  6Q GAIN WILD-TYPE       1      118       125      123
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               11               118
  STAGE III              15               125
  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         14  18   5
  6Q GAIN WILD-TYPE      109 177  53
D12V4, multiclass
          clus
vv         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1+T2              14               109
  T3                    18               177
  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
  6Q GAIN MUTATED    21   6   4   2
  6Q GAIN WILD-TYPE 215  41  71   6
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              21               215
  N1               6                41
  N2               4                71
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    19   1
  6Q GAIN WILD-TYPE 173  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     19    1
  6Q GAIN WILD-TYPE  173   10
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              19               173
  1               1                10
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     6  33
  6Q GAIN WILD-TYPE 101 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6   33
  6Q GAIN WILD-TYPE  101  268
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               6               101
  MALE                33               268
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    30   5
  6Q GAIN WILD-TYPE 334  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     30    5
  6Q GAIN WILD-TYPE  334   15
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               30               334
  YES               5                15
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, continuous
D12V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       4                         0    35
  6Q GAIN WILD-TYPE    39                        22   292
D12V12, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   4                39
  BLACK OR AFRICAN AMERICAN               0                22
  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"
D12V13, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  37
  6Q GAIN WILD-TYPE   9 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   37
  6Q GAIN WILD-TYPE    9  332
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  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    95  76
  7P GAIN WILD-TYPE 132 102
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              171               234 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               76               102 
$`7P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
       20.48        25.94        28.70        12.92         4.90        18.48 
TCGA-CU-A72E TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU 
       13.58       130.88        87.32         8.22        50.27        23.21 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L 
       66.05        17.98        64.18        67.36        36.66        38.24 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
      165.73       166.03        11.18        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
        1.22         4.01        46.78        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       26.73        58.92         6.28         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY 
        3.06         9.67        31.07        17.23        11.08        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK 
       70.32        21.40        10.92        32.98        19.82        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-KQ-A41P TCGA-S5-A6DX TCGA-SY-A9G0 
        8.58        22.72         9.01        35.97         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       86.83        51.32        97.45        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T5 
       15.98        14.93         4.21        21.04         2.24        66.64 
TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-AA4R TCGA-4Z-AA7R 
       71.57        98.99        18.58        13.64        34.06        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 
       27.62         0.62        41.75        10.22        47.80        40.08 
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42E 
        2.66         6.58        12.16        17.16        16.18        36.43 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A5U8 
       28.41        23.01        12.79        12.13        12.16        13.12 
TCGA-DK-A1A3 TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       21.86        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-E5-A2PC TCGA-E7-A4IJ 
        8.15        15.02        18.81        19.00        43.59        22.16 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3N5 
       24.03        13.68         8.09        32.02         8.94        22.52 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TF 
       22.98        20.91         5.36        27.45         7.10         2.27 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 
       10.65         3.25        59.31        66.02        29.36        20.71 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 
       15.91        14.07        13.91        26.70        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A766 TCGA-GU-AATQ TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE 
       11.31        15.78         7.00        19.40        38.60        12.16 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41S TCGA-LC-A66R 
        9.07        11.70         1.81        16.27         1.15        15.32 
TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC 
       13.48        38.99        22.68        76.01        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SU 
       35.24        29.56         6.21        48.62        79.66         5.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-ZF-A9R0 TCGA-ZF-A9R3 
      110.60         2.96        56.48        75.39        22.36        31.20 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V 
       13.41        64.08        58.72        20.22         2.89        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5H 
       67.20         8.52        29.49 

$`7P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL 
      108.95        14.89         8.35         9.96         8.98        18.58 
TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IQ 
       15.12         2.14        19.00        16.70        46.68        17.72 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
       21.30         9.67        53.29        76.60        15.68        50.70 
TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-FD-A3B6 
       52.01        13.64        13.64        56.15        20.32        33.04 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SR 
       60.66        24.30        23.41        17.98        29.16        19.79 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       15.58        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TH TCGA-G2-A2ES TCGA-GC-A3RB TCGA-GC-A3WC 
       62.86        18.81         4.31        33.01        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A40G TCGA-K4-A3WS TCGA-K4-A3WU 
       24.92        32.78        20.28        19.07        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q 
        2.76         9.14        27.68        52.73        50.56        46.98 
TCGA-R3-A69X TCGA-XF-A8HE TCGA-XF-A9SM TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 
       14.24       125.49        34.45        12.76        11.90        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       18.90         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        7.63        91.73        44.32        30.94        61.45        86.30 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        3.88         9.63        21.11        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       88.87        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        16.83        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I 
       50.04        51.16        66.54         2.50        17.42         7.33 
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.74        13.15        19.04        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0F0 
       14.96         5.06         8.25         4.67        17.56         1.94 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       12.56        13.97        12.59        13.08        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.62        12.26        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        11.34        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
        1.84        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6X 
       15.62        20.81        10.55       163.30        13.58        15.35 
TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       12.03        38.83        29.72         5.36         2.24        16.70 
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-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B8 
       14.07        12.95        15.32        14.37        16.77        12.62 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62N 
       27.98         5.52        25.74        14.96        19.33         2.70 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ 
       13.35        10.85        12.66         8.94        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO 
       15.95        26.93         7.23        20.12         6.94        15.81 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42R TCGA-GU-A762 
        0.49         8.94         2.10         3.12        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       20.05         4.73        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6MB 
       36.49         1.51        64.01        21.24        17.72        15.42 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80        44.38        15.58        21.07        12.23        16.67 
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-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
        3.85        45.04         6.58         1.87        17.88        64.80 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW 
       66.41        23.64        28.24        16.27        92.98         8.32 
TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
        6.77        27.06        18.84         0.66        11.97        25.41 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA4W 
       35.84        21.86        28.41        47.84         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       56.35        35.41        19.40        54.21         5.52        10.65 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.62              0.49 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           166.03            163.30 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           18.580            17.125 
[1] "0.6 - 166.0 (18.6)" "0.5 - 163.3 (17.1)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         1       42        61       66
  7P GAIN WILD-TYPE       1       87        79       69
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               42                87
  STAGE III              61                79
  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
  7P GAIN MUTATED         42  87  30
  7P GAIN WILD-TYPE       81 108  28
D13V4, multiclass
          clus
vv         7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1+T2              42                81
  T3                    87               108
  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    89  24  33   7
  7P GAIN WILD-TYPE 147  23  42   1
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              89               147
  N1              24                23
  N2              33                42
  N3               7                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    77   5
  7P GAIN WILD-TYPE 115   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     77    5
  7P GAIN WILD-TYPE  115    6
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              77               115
  1               5                 6
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    45 126
  7P GAIN WILD-TYPE  62 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     45  126
  7P GAIN WILD-TYPE   62  175
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              45                62
  MALE               126               175
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   157   5
  7P GAIN WILD-TYPE 207  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    157    5
  7P GAIN WILD-TYPE  207   15
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              157               207
  YES               5                15
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, continuous
D13V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED      11                         9   144
  7P GAIN WILD-TYPE    32                        13   183
D13V12, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                  11                32
  BLACK OR AFRICAN AMERICAN               9                13
  WHITE                                 144               183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    80  67
  7Q GAIN WILD-TYPE 147 111
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              147               258 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               67               111 
$`7Q GAIN MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A2LD 
       16.77        15.12        33.83        12.39        26.14        20.48 
TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A2HX 
       25.94        12.92         4.90        18.48        13.58        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6B1 
       87.32         8.22        50.27        23.21        17.98        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 
       36.66        38.24       165.73       166.03        13.64        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B7 TCGA-FD-A3SQ 
       20.32        15.35        25.58         0.92         4.01        46.78 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5C1 TCGA-FD-A62P 
       12.85        27.35         3.62        26.73        58.92         6.28 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P 
        6.15        12.69         4.31         9.67        17.23        11.08 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.62        70.32        21.40        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-KQ-A41P 
       27.35         8.58        19.07        22.72         9.01        35.97 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
        1.84        33.14        86.83        51.32        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9T5 TCGA-XF-AAMQ 
       97.12        15.35         3.22        14.93        66.64        71.57 
TCGA-XF-AAMY TCGA-ZF-AA4R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA87 
       98.99        34.06        27.62         0.62        41.75        47.80 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42E 
       40.08         2.66         6.58        17.16        16.18        36.43 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CF-A5U8 TCGA-DK-A1AD 
       28.41        23.01        12.79        12.13        13.12       112.44 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-AA6T TCGA-DK-AA6U TCGA-E5-A2PC 
       17.95         7.79        13.58        18.81        19.00        43.59 
TCGA-E7-A4IJ TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 
       22.16        13.68         8.09        16.77         8.94        22.52 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TF 
       22.98        20.91         5.36        27.45         7.10         2.27 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 
       10.65         3.25        59.31        66.02        29.36        20.71 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GU-A764 
       15.91        14.07        13.91        26.70        20.98        20.05 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P 
       19.40        38.60        21.24        11.70         1.81        16.27 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78M 
       44.38         1.15        15.32        13.48        38.99        22.68 
TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A9SG 
       76.01         3.02        29.56         6.21         6.58        48.62 
TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
       79.66         5.98       110.60         6.77        56.48        75.39 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RN 
       22.36        31.20        28.41        13.41        58.72        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA5H 
        2.89        67.20        29.49 

$`7Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PK TCGA-BT-A42C 
      108.95        16.27        14.89         8.35         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
        8.98        18.58        15.12         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV 
      130.88        17.72        21.30         9.67        66.05        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA71 
       53.29        76.60        15.68        50.70        52.01        13.64 
TCGA-DK-AA74 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       56.15         1.22        33.04        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       17.98        29.16        19.79        15.58        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE 
        5.69         8.25        18.08        62.86        18.81        12.36 
TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
        3.06        31.07        33.01        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       10.92        32.78        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-XF-A9SK 
       27.68        52.73        50.56        46.98        14.24        15.98 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       34.45         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90         2.24         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       54.90         7.63        91.73        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 
       30.28        94.29         3.48        88.87        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         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-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM 
       66.54        10.22         2.50        17.42         7.33         6.74 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0F0 
       14.96         5.06         8.25         4.67        17.56         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-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.34        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE 
       29.79         1.84        21.86        66.41        18.41        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW 
       17.62        15.62       142.78         4.80         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA76 
       10.55       163.30        15.02        13.58        15.35        12.03 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        29.72         5.36         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-A3B8 
       14.07        12.95        15.32        14.37        32.02        12.62 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62N 
       27.98         5.52        25.74        14.96        19.33         2.70 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ 
       13.35        10.85        12.66         8.94        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO 
       15.95        26.93         7.23        20.12         6.94        15.81 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
        0.49         8.94         2.10         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
       18.97         7.63        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF 
       21.34        19.10         8.48        36.49         1.51        64.01 
TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LT-A5Z6 
       12.16         9.07        17.72        15.42        11.80        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L 
       21.07        12.23        16.67        16.54        17.62        37.05 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       78.25        69.34       112.83        35.24        17.82         3.85 
TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX 
       45.04         1.87        17.88        64.80        66.41        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 
       28.24        16.27        92.98         2.96         8.32        27.06 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.84         0.66        11.97        25.41        35.84        21.86 
TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
       64.08        47.84         8.61        59.38        60.16        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       35.41        19.40         8.52        54.21         5.52        10.65 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.62              0.49 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           166.03            163.30 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            20.28             16.27 
[1] "0.6 - 166.0 (20.3)" "0.5 - 163.3 (16.3)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         1       40        48       58
  7Q GAIN WILD-TYPE       1       89        92       77
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               40                89
  STAGE III              48                92
  STAGE IV               58                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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         42  69  27
  7Q GAIN WILD-TYPE       81 126  31
D14V4, multiclass
          clus
vv         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1+T2              42                81
  T3                    69               126
  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
  7Q GAIN MUTATED    76  19  31   7
  7Q GAIN WILD-TYPE 160  28  44   1
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              76               160
  N1              19                28
  N2              31                44
  N3               7                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    42 106
  7Q GAIN WILD-TYPE  65 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     42  106
  7Q GAIN WILD-TYPE   65  195
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              42                65
  MALE               106               195
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   136   6
  7Q GAIN WILD-TYPE 228  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    136    6
  7Q GAIN WILD-TYPE  228   14
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              136               228
  YES               6                14
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, continuous
D14V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       9                         9   125
  7Q GAIN WILD-TYPE    34                        13   202
D14V12, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN               9                13
  WHITE                                 125               202
[1] 3 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     3 132
  7Q GAIN WILD-TYPE   6 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3  132
  7Q GAIN WILD-TYPE    6  237
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             132               237
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    52  38
  8P GAIN WILD-TYPE 175 140
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               90               315 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               38               140 
$`8P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-CU-A72E 
       16.27        15.12        33.83        12.39        26.14        13.58 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA71 
       17.72        50.27        17.98        36.66       165.73        13.64 
TCGA-DK-AA74 TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A6TI TCGA-G2-A2ES 
       56.15        53.88         5.69        58.92         9.67        33.01 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GV-A6ZA TCGA-KQ-A41P TCGA-S5-A6DX TCGA-UY-A78N 
       17.62        21.40        22.72        35.97         1.84        86.83 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SP TCGA-XF-A9SY TCGA-XF-A9T6 
       97.45        97.12        15.35        14.93        21.04         2.10 
TCGA-XF-AAMY TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-4Z-AA7N TCGA-4Z-AA81 
       98.99        18.58        13.64        21.11        44.94        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20V 
       51.16        47.80        40.08         6.74        19.04         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-A47X TCGA-CF-A5UA TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A3WX 
       12.62        12.00        66.41        16.14        17.95        10.55 
TCGA-DK-AA6P TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A85H TCGA-E7-A97P 
       15.02        43.59        22.16        24.03        12.95        14.37 
TCGA-FD-A3N6 TCGA-FD-A43U TCGA-FD-A62O TCGA-FD-A62S TCGA-FJ-A3ZE TCGA-G2-AA3B 
       27.98        20.91         7.10        13.35        10.65        66.02 
TCGA-GC-A3I6 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A2OF 
       20.71         7.00        14.27        36.49        38.60        64.01 
TCGA-K4-A5RI TCGA-K4-A83P TCGA-KQ-A41S TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78M 
       11.70        16.27         1.15        13.48        38.99        22.68 
TCGA-UY-A8OC TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SU 
        3.02         6.21         3.85        48.62        64.80         5.98 
TCGA-ZF-A9R3 TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       31.20        20.22         2.89        67.20        56.35        35.41 

$`8P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ 
      108.95        16.77        14.89         8.35        20.48        25.94 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
        9.96        28.70         8.98        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       15.12        18.48         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       46.68        87.32         8.22        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       66.05        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 
       50.70        38.24        52.01       166.03        13.64        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y 
       46.78        19.79        12.85        27.35         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA 
       26.73        10.78         8.25        18.08         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
       31.07        17.23        11.08        70.32        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       27.35         8.58        19.07         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q 
        2.76         9.14        27.68        52.73        50.56        46.98 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A9SJ TCGA-XF-A9SK 
       14.24        33.14        51.32       125.49         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 
       34.45         4.21        12.76        11.90        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24        66.64        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
        7.63        71.57        91.73        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       86.30         3.88         9.63        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       88.87        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7R 
       11.97        94.88       104.65         8.35        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA83 TCGA-4Z-AA86 
       34.98        27.62        50.04         0.62        66.54        10.22 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX 
        2.50        17.42         7.33         2.66         6.58        13.15 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X 
       12.16        17.88        19.50         5.06        14.96         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS 
       16.18         4.67        17.56        28.41        12.79        12.56 
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-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.10        12.26        13.12        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.41       112.44        17.62        15.62         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q 
        4.80        13.58         8.15        20.81       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 
       18.81        19.00        15.35        12.03        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        5.36         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
       26.24         4.24        24.66        13.68        14.07        15.32 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV 
        5.52        25.74        22.98        14.96        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 
       27.45         2.70         2.27        10.85        12.66         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25        61.94        48.00        15.95        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-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07         0.49         8.94        13.91        26.70         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-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       20.05        15.78         4.73        21.34        19.10         8.48 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ 
        1.51        19.40        12.16        21.24         9.07        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42        11.80        44.38        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L 
       21.07        12.23        16.67        16.54        17.62        37.05 
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        35.24        29.56 
TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI 
       17.82        45.04         6.58         1.87        17.88        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
       66.41        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R5 
       18.84         0.66        11.97        22.36        25.41        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
        8.61        59.38        60.16        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.15              0.49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           165.73            166.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            19.63             17.16 
[1] "1.1 - 165.7 (19.6)" "0.5 - 166.0 (17.2)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         1       28        34       26
  8P GAIN WILD-TYPE       1      101       106      109
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               28               101
  STAGE III              34               106
  STAGE IV               26               109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  8P GAIN MUTATED         31  42  12
  8P GAIN WILD-TYPE       92 153  46
D15V4, multiclass
          clus
vv         8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1+T2              31                92
  T3                    42               153
  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
  8P GAIN MUTATED    50  12  12   2
  8P GAIN WILD-TYPE 186  35  63   6
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              50               186
  N1              12                35
  N2              12                63
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    47   3
  8P GAIN WILD-TYPE 145   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     47    3
  8P GAIN WILD-TYPE  145    8
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              47               145
  1               3                 8
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    22  68
  8P GAIN WILD-TYPE  85 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     22   68
  8P GAIN WILD-TYPE   85  233
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              22                85
  MALE                68               233
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    81   5
  8P GAIN WILD-TYPE 283  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     81    5
  8P GAIN WILD-TYPE  283   15
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               81               283
  YES               5                15
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, continuous
D15V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED      11                         5    67
  8P GAIN WILD-TYPE    32                        17   260
D15V12, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                  11                32
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                  67               260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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   112  87
  8Q GAIN WILD-TYPE 115  91
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              199               206 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               87                91 
$`8Q GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W 
       16.27        15.12        33.83        12.39        26.14         8.35 
TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AC TCGA-DK-A2I6 
        8.98        12.92        18.48        13.58       130.88        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 
        8.22        17.72        50.27        23.21        66.05        17.98 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       15.68        36.66        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU 
       13.64        56.15        11.18        20.32        25.58         0.92 
TCGA-FD-A3B6 TCGA-FD-A3SQ TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       33.04        46.78        26.73        53.88        10.78         5.69 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
       18.08        58.92         6.28        12.69        12.36         4.31 
TCGA-FD-A6TI TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
        9.67        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-HQ-A5ND 
       17.75        32.98        19.82        20.28        22.72         9.01 
TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41P TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
        2.76        52.73        35.97         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP 
       51.32        97.45        97.12        15.35         3.22        14.93 
TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMH 
       12.76        21.04        26.27         2.24         2.10        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3M 
       54.90         7.63        98.99        61.45        18.58        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KP 
       21.11        30.28         3.48        57.90        24.13        11.97 
TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 
       44.94        17.16         0.62        41.75        51.16        10.22 
TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20X 
       47.80        40.08         6.74        19.04         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C 
       17.16        16.18        36.43         1.94        23.01        13.97 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY 
       12.13        13.08        10.95        12.62        12.00        11.34 
TCGA-CF-A9FF TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       11.87         5.19         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3WX TCGA-DK-AA6P 
      112.44        16.14        17.95       142.78        10.55        15.02 
TCGA-DK-AA6U TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7PW 
       19.00        43.59        38.83        22.16        24.03        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3N6 TCGA-FD-A43N TCGA-FD-A43U 
       12.95        14.37         8.09        27.98        22.98        20.91 
TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A62S TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        5.36         7.10        13.35        12.66        10.65         3.25 
TCGA-G2-A2EK TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.95        66.02        20.71         2.10         3.12        20.98 
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-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ 
       38.60        64.01        12.16         9.07        11.70         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A8JT TCGA-MV-A51V 
       15.42        16.27        44.38         1.15        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OB 
       12.23        16.67        38.99        17.62        22.68        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
        3.02       112.83        29.56         6.21         3.85        45.04 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAMG TCGA-XF-AAMT 
       48.62        64.80        79.66         5.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
        8.32        75.39        18.84        22.36        25.41        31.20 
TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       28.41        58.72        20.22         2.89         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5N 
        5.52 

$`8Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
      108.95        16.77        14.89        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A1AA 
       28.70        18.58         4.90        15.12         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6AW 
       16.70        46.68        21.30         9.67        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-E5-A4TZ TCGA-E7-A7DV 
       76.60        67.36        50.70        38.24        15.35         1.22 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BY 
       19.79        12.85        27.35         3.62        15.58         8.25 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       62.86        18.81         6.15         3.06        31.07        17.23 
TCGA-FT-A61P TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A40E 
       11.08        24.92        10.92        32.78        27.35         8.58 
TCGA-GV-A40G TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O 
       19.07        25.02         3.45         9.14        27.68        50.56 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-XF-A8HE TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST 
       46.98        14.24       125.49        15.98        34.45         4.21 
TCGA-XF-A9SW TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMQ 
       11.90        18.90        66.64        13.74        10.82        71.57 
TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 
       91.73        44.32        30.94        86.30         3.88         9.63 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KQ 
       94.29        88.87        34.06        19.69        12.23        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
      104.65         8.35        16.83        34.98        27.62        50.04 
TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 
       66.54         2.50        17.42         7.33         2.66         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       13.15        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF 
        4.67        17.56        28.41        12.79        12.56        12.59 
TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       12.16        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A3YL TCGA-DK-A1AF TCGA-DK-A1AG 
       12.10        11.34        13.08        29.79        17.62        15.62 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY 
        7.79         4.80        13.58         8.15        20.81       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.58        18.81        15.35        12.03        29.72         5.36 
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-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 
        4.24        24.66        14.07        15.32        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S 
        8.94        12.62        22.52         5.52        25.74        14.96 
TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A871 
       19.33        27.45         2.70         2.27        10.85         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        48.00        26.93        59.31         7.23        20.12 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW 
        6.94        29.36        15.81        15.91        14.07         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        8.94        13.91        26.70         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.63        20.05        15.78         4.73         1.51        19.40 
TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-S5-AA26 
       21.24        17.72        11.80        15.32        15.58        16.54 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A9PA TCGA-UY-A9PD TCGA-XF-A8HC 
       37.05        76.01        78.25        35.24        17.82         6.58 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
        1.87        17.88        66.41        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L 
       92.98         6.77        56.48        27.06         0.66        11.97 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-AA4V 
       35.84        21.86        13.41        64.08        47.84        59.38 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.62              0.49 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           166.03            163.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            18.41             16.77 
[1] "0.6 - 166.0 (18.4)" "0.5 - 163.3 (16.8)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         1       62        71       64
  8Q GAIN WILD-TYPE       1       67        69       71
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               62                67
  STAGE III              71                69
  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
  8Q GAIN MUTATED         64 96 27
  8Q GAIN WILD-TYPE       59 99 31
D16V4, multiclass
          clus
vv         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1+T2              64                59
  T3                    96                99
  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
  8Q GAIN MUTATED   113  25  32   4
  8Q GAIN WILD-TYPE 123  22  43   4
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             113               123
  N1              25                22
  N2              32                43
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    51 149
  8Q GAIN WILD-TYPE  56 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     51  149
  8Q GAIN WILD-TYPE   56  152
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              51                56
  MALE               149               152
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   177  12
  8Q GAIN WILD-TYPE 187   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    177   12
  8Q GAIN WILD-TYPE  187    8
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              177               187
  YES              12                 8
[1] 2 2
[1] FALSE
D16V9, continuous
D16V10, continuous
D16V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED      18                         9   161
  8Q GAIN WILD-TYPE    25                        13   166
D16V12, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                  18                25
  BLACK OR AFRICAN AMERICAN               9                13
  WHITE                                 161               166
[1] 3 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     5 173
  8Q GAIN WILD-TYPE   4 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5  173
  8Q GAIN WILD-TYPE    4  196
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 4
  NOT HISPANIC OR LATINO             173               196
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    43  26
  9P GAIN WILD-TYPE 184 152
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               69               336 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               26               152 
$`9P GAIN MUTATED`
TCGA-4Z-AA7Q TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-CU-A0YR TCGA-DK-A1AC TCGA-DK-A2I6 
       16.77        25.94        12.92        15.12       130.88        87.32 
TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-FD-A3B6 TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A5BT 
       36.66       165.73        33.04        23.41        27.35        10.78 
TCGA-FD-A6TH TCGA-G2-AA3D TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A40G TCGA-SY-A9G0 
        4.31        70.32        32.78        19.82        19.07        33.14 
TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SY TCGA-XF-A9T3 
       97.45        15.35        34.45        14.93        21.04         2.24 
TCGA-XF-AAML TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-4Z-AA7R 
        7.63        13.64        30.28        19.69        24.13        17.16 
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CU-A3QU TCGA-DK-A1AD 
       40.08         6.74        17.16         1.94         5.19       112.44 
TCGA-DK-A2I1 TCGA-DK-A3IM TCGA-FD-A3B3 TCGA-FD-A3N5 TCGA-FD-A62N TCGA-FD-A6TF 
       17.95         8.15        32.02        22.52         2.70         2.27 
TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GD-A2C5 
       10.65        61.94        48.00        20.71        15.91        26.70 
TCGA-GD-A3OP TCGA-GV-A3QI TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-LC-A66R TCGA-UY-A78K 
        2.10        36.49        12.16         1.81        15.32        17.62 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A9SG TCGA-XF-AAN5 
       76.01        78.25        29.56         6.58        48.62        75.39 
TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N 
       22.36        21.86        64.08        58.72        47.84         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA58 
       59.38        67.20        54.21 

$`9P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
       14.89         8.35        20.48         9.96        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       18.58         4.90        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       16.70        46.68         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M 
       76.60        67.36        15.68        50.70        38.24        52.01 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      166.03        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA 
       15.35        25.58         0.92         1.22         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        15.58        26.73        53.88         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.69        12.36         3.06         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       11.08        33.01        17.62        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       24.92        10.92        32.98        20.28        27.35         8.58 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SJ 
        1.84        86.83        51.32       125.49        97.12         3.22 
TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 
       15.98         4.21        12.76        11.90        26.27        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RC 
       86.30        18.58         3.88         9.63        21.11        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP 
        3.48        88.87        34.06        57.90        12.23        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        16.83        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-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80         2.50        17.42         7.33         2.66 
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-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
        5.06        14.96         5.06         8.25        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       17.56        36.43        28.41        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-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE 
       29.79         1.84        21.86        66.41        18.41        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62        15.62         7.79       142.78         4.80        13.58 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        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-A7PW 
       26.96        26.24         4.24        24.03        24.66        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-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
        8.94        12.62        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O 
       14.96        20.91        19.33         5.36        27.45         7.10 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK 
       13.35        10.85        12.66         8.94         3.25        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        59.31         7.23        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       29.36        15.81        14.07         0.49         8.94        13.91 
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-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.10         8.48         1.51        19.40        38.60        64.01 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
       21.24         9.07        11.70        17.72        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       11.80        44.38         1.15        15.58        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M 
       12.23        16.67        16.54        38.99        37.05        22.68 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE 
       69.34         3.02       112.83        35.24        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85        45.04         1.87        17.88        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       18.84         0.66        11.97        25.41        31.20        35.84 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 
       28.41        13.41        20.22         8.61        60.16        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       35.41        19.40         8.52        29.49         5.52        10.65 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.81              0.49 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           165.73            166.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            22.36             16.70 
[1] "1.8 - 165.7 (22.4)" "0.5 - 166.0 (16.7)"
[1] "hr=" "1.5"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         1       21        24       23
  9P GAIN WILD-TYPE       1      108       116      112
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               21               108
  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
  9P GAIN MUTATED         20  33   9
  9P GAIN WILD-TYPE      103 162  49
D17V4, multiclass
          clus
vv         9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1+T2              20               103
  T3                    33               162
  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    37   5  15   2
  9P GAIN WILD-TYPE 199  42  60   6
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              37               199
  N1               5                42
  N2              15                60
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    31   3
  9P GAIN WILD-TYPE 161   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     31    3
  9P GAIN WILD-TYPE  161    8
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              31               161
  1               3                 8
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15  54
  9P GAIN WILD-TYPE  92 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15   54
  9P GAIN WILD-TYPE   92  247
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              15                92
  MALE                54               247
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    59   2
  9P GAIN WILD-TYPE 305  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     59    2
  9P GAIN WILD-TYPE  305   18
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               59               305
  YES               2                18
[1] 2 2
[1] FALSE
D17V9, continuous
D17V10, continuous
D17V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       2                         3    60
  9P GAIN WILD-TYPE    41                        19   267
D17V12, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   2                41
  BLACK OR AFRICAN AMERICAN               3                19
  WHITE                                  60               267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  61
  9P GAIN WILD-TYPE   7 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   61
  9P GAIN WILD-TYPE    7  308
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              61               308
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    34  21
  9Q GAIN WILD-TYPE 193 157
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               55               350 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               157 
$`9Q GAIN MUTATED`
TCGA-4Z-AA84 TCGA-CU-A0YN TCGA-DK-A1AC TCGA-DK-A3IN TCGA-DK-A6B6 TCGA-DK-AA6M 
       15.12        12.92       130.88         8.22        36.66        52.01 
TCGA-DK-AA6R TCGA-FD-A3SL TCGA-FD-A5BT TCGA-FD-A6TD TCGA-FD-A6TH TCGA-G2-AA3D 
      165.73        23.41        10.78        12.69         4.31        70.32 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9T3 TCGA-ZF-A9R4 
       17.75        24.92        97.45        15.35         2.24        30.28 
TCGA-ZF-AA4T TCGA-4Z-AA7R TCGA-4Z-AA82 TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A2LA 
       19.69        17.16        51.16        40.08         6.74        17.16 
TCGA-C4-A0F0 TCGA-DK-A2I1 TCGA-DK-A3IM TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A5BV 
        1.94        17.95         8.15        32.02        16.77         5.36 
TCGA-FD-A62N TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-GC-A3I6 
        2.70        10.85        10.65        61.94        48.00        20.71 
TCGA-GC-A3RC TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-LC-A66R TCGA-UY-A78K 
       15.91        19.40        12.16         1.81        15.32        17.62 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A9SG 
       78.25        69.34        29.56         6.21         6.58        48.62 
TCGA-XF-AAN5 TCGA-ZF-A9R7 TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4V 
       75.39        21.86        58.72        47.84         2.89        59.38 
TCGA-ZF-AA58 
       54.21 

$`9Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
        8.98        18.58         4.90        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ 
        2.14        19.00        16.70        46.68        87.32        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        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-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       38.24       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        4.01        60.66        24.30        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       19.79        12.85        27.35         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       53.88         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI 
       62.86        18.81         6.15        12.36         3.06         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM 
       31.07        17.23        11.08        33.01        17.62        21.40 
TCGA-GC-A3RB TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       19.13        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       51.32       125.49        97.12         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       13.64        21.11        94.29         3.48        88.87        34.06 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
        8.35        44.94        16.83        34.98        27.62        50.04 
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-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       17.42         7.33         2.66         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-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        8.25        16.18         4.67        17.56        36.43        28.41 
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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW 
       15.62         7.79       142.78         4.80        13.58        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       10.55       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.35        12.03        43.59        38.83        29.72         5.36 
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-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B8 
       12.95        15.32        14.37         8.09         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
       20.91        19.33        27.45         7.10        13.35         2.27 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       12.66         8.94         3.25        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
        7.23        20.12        66.02         6.94        29.36        15.81 
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        26.70         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-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.10         8.48        36.49         1.51        38.60        64.01 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
       21.24         9.07        11.70        17.72        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       11.80        44.38         1.15        15.58        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M 
       12.23        16.67        16.54        38.99        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       76.01         3.02       112.83        35.24        17.82         3.85 
TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
       45.04         1.87        17.88        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A89H 
        2.96         8.32         6.77        56.48        27.06        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W 
       28.41        13.41        64.08        20.22         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       67.20        56.35        35.41        19.40         8.52        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.81              0.49 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           165.73            166.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            17.95             17.59 
[1] "1.8 - 165.7 (17.9)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         1       14        23       18
  9Q GAIN WILD-TYPE       1      115       117      117
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 1                 1
  STAGE II               14               115
  STAGE III              23               117
  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         12  29   7
  9Q GAIN WILD-TYPE      111 166  51
D18V4, multiclass
          clus
vv         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1+T2              12               111
  T3                    29               166
  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    34   4  11   1
  9Q GAIN WILD-TYPE 202  43  64   7
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              34               202
  N1               4                43
  N2              11                64
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    22   4
  9Q GAIN WILD-TYPE 170   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     22    4
  9Q GAIN WILD-TYPE  170    7
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              22               170
  1               4                 7
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    16  40
  9Q GAIN WILD-TYPE  91 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     16   40
  9Q GAIN WILD-TYPE   91  261
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              16                91
  MALE                40               261
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    49   1
  9Q GAIN WILD-TYPE 315  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     49    1
  9Q GAIN WILD-TYPE  315   19
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               49               315
  YES               1                19
[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  60
  10P GAIN WILD-TYPE 170 118
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               117                288 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                60                118 
$`10P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A3PJ 
       16.27        16.77        15.12        26.14         8.35        25.94 
TCGA-CU-A0YN TCGA-DK-A1A5 TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A6B2 
       12.92         2.14        87.32         8.22        66.05        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SS 
       36.66       166.03        33.04        60.66        24.30        12.85 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FD-A6TG 
       26.73        53.88        18.08        58.92        12.36         3.06 
TCGA-FD-A6TI TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3RB TCGA-GU-A42P TCGA-GU-AATP 
        9.67        11.08        33.01        19.13        10.92        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       19.82        20.28         8.58        22.72         9.01        25.02 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41P TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HF 
        9.14        27.68        35.97        86.83        51.32        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-AAMH TCGA-XF-AAML 
       15.35         3.22        15.98        14.93        11.31         7.63 
TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-2F-A9KO 
       13.64        30.28        94.29        34.06        57.90        24.13 
TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J 
       17.16         0.62        41.75         2.50        40.08         2.66 
TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A42E TCGA-CF-A1HS 
        6.58         5.06         5.06        16.18        36.43        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A5UA TCGA-DK-A1A3 TCGA-DK-A1A6 
       12.59        12.13        12.16        12.00        21.86        66.41 
TCGA-DK-A1AD TCGA-DK-A3IL TCGA-DK-AA6P TCGA-E5-A4U1 TCGA-E7-A6MD TCGA-E7-A6ME 
      112.44        13.58        15.02        38.83         4.24        24.03 
TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FT-A3EE 
       13.68        14.37         8.09        27.45         2.27         3.25 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A6C6 
       20.12        66.02        29.36         0.49        26.70         2.20 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QH TCGA-HQ-A2OE TCGA-HQ-A2OF 
        4.73         7.00        21.34         8.48        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41S TCGA-SY-A9G5 TCGA-UY-A78K 
       12.16        17.72         1.81         1.15        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A9PA TCGA-XF-A9SH TCGA-XF-AAMG 
       37.05        22.68        69.34        35.24        64.80       110.60 
TCGA-XF-AAMT TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RN 
        2.96        22.36        31.20        28.41        64.08        20.22 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-GU-AATO 
       35.41        19.40        10.65 

$`10P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A3PK 
      108.95        33.83        12.39        14.89        20.48         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       28.70         8.98        18.58         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IQ 
       13.58        19.00        16.70       130.88        46.68        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV 
       50.27        21.30        23.21         9.67        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M 
       53.29        76.60        67.36        50.70        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      165.73        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SL 
       15.35        25.58         0.92         1.22         4.01        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X 
       17.98        29.16        46.78        19.79        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TA 
       15.58        10.78         5.69         8.25         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       18.81         6.15        12.69         4.31        31.07        17.23 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A763 
       17.62        70.32        21.40        17.75        24.92        32.78 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41O 
       27.35        19.07         3.45         2.76        52.73        50.56 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HD TCGA-XF-A8HE 
       46.98        14.24         1.84        33.14        97.45       125.49 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       34.45         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       54.90        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 
       61.45        86.30        18.58         3.88         9.63        21.11 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ 
        3.48        88.87        19.69        12.23        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W 
      104.65         8.35        44.94        16.83        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM 
       50.04        51.16        66.54        10.22        47.80        17.42 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        7.33         6.74        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B 
       19.50        14.96         8.25        17.16         4.67        17.56 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MH 
       28.41         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-A9FM 
       13.12        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF 
        5.19        29.79         1.84        18.41        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
       15.62        17.95         7.79       142.78         4.80         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       20.81        10.55       163.30        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       15.35        12.03        43.59        29.72         5.36        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-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 
       24.66        14.07        12.95        15.32        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N 
       22.98        14.96        20.91        19.33         5.36         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        7.10        13.35        10.85        12.66        10.65         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
        6.94        20.71        15.81        15.91        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R 
       13.91         2.10         3.12        20.98        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI 
        7.63        20.05        15.78        14.27        19.10        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB 
        1.51        19.40        21.24         9.07        11.70        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       16.27        11.80        44.38        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P 
       13.48        12.23        16.67        16.54        76.01        78.25 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
        3.02       112.83        29.56        17.82         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI 
       45.04         6.58         1.87        17.88        48.62        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
        8.32         6.77        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
        0.66        11.97        25.41        35.84        21.86        13.41 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       58.72        47.84         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       67.20        56.35         8.52        54.21        29.49         5.52 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.49               0.56 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            166.03             165.73 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             19.13              17.49 
[1] "0.5 - 166.0 (19.1)" "0.6 - 165.7 (17.5)"
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         1       33        38       44
  10P GAIN WILD-TYPE       1       96       102       91
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  1                  1
  STAGE II                33                 96
  STAGE III               38                102
  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         35  59  16
  10P GAIN WILD-TYPE       88 136  42
D19V4, multiclass
          clus
vv         10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1+T2               35                 88
  T3                     59                136
  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
  10P GAIN MUTATED    52  17  23   4
  10P GAIN WILD-TYPE 184  30  52   4
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               52                184
  N1               17                 30
  N2               23                 52
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    54   3
  10P GAIN WILD-TYPE 138   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     54    3
  10P GAIN WILD-TYPE  138    8
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               54                138
  1                3                  8
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    23  94
  10P GAIN WILD-TYPE  84 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     23   94
  10P GAIN WILD-TYPE   84  207
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               23                 84
  MALE                 94                207
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   103   4
  10P GAIN WILD-TYPE 261  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    103    4
  10P GAIN WILD-TYPE  261   16
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO               103                261
  YES                4                 16
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, continuous
D19V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED      10                         2    98
  10P GAIN WILD-TYPE    33                        20   229
D19V12, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                   10                 33
  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     3 100
  10P GAIN WILD-TYPE   6 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3  100
  10P GAIN WILD-TYPE    6  269
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              100                269
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    17  27
  10Q GAIN WILD-TYPE 210 151
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                44                361 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                27                151 
$`10Q GAIN MUTATED`
TCGA-4Z-AA84 TCGA-DK-A3IN TCGA-DK-A6B2 TCGA-FD-A3B6 TCGA-FD-A3SS TCGA-FD-A5BR 
       15.12         8.22        15.68        33.04        12.85        26.73 
TCGA-FD-A6TI TCGA-GC-A3RB TCGA-HQ-A5ND TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HG 
        9.67        19.13         9.01        86.83        51.32        15.35 
TCGA-XF-A9SK TCGA-XF-AAMH TCGA-ZF-AA4R TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-4Z-AA81 
       15.98        11.31        34.06        24.13         0.62        41.75 
TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20V TCGA-CF-A3MF TCGA-CF-A3MI TCGA-DK-A1A3 
        6.58         5.06         5.06        12.59        12.16        21.86 
TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-E5-A4U1 TCGA-E7-A6MD TCGA-E7-A7PW TCGA-E7-A97Q 
       66.41       112.44        38.83         4.24        13.68         8.09 
TCGA-FD-A5BZ TCGA-G2-AA3B TCGA-GU-A767 TCGA-GU-AATQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       27.45        66.02         4.73         7.00        38.60        64.01 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-XF-AAMG TCGA-XF-AAMT TCGA-ZF-A9R3 TCGA-ZF-A9R9 
       38.99        22.68       110.60         2.96        31.20        28.41 
TCGA-ZF-A9RN TCGA-GU-AATO 
       20.22        10.65 

$`10Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       87.32        17.72        50.27        21.30        23.21         9.67 
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-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       25.58         0.92         1.22         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P 
       23.41        17.98        29.16        46.78        19.79        27.35 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        15.58        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.69        12.36         3.06         4.31        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC 
       11.08        33.01        17.62        70.32        21.40        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU 
       27.35         8.58        19.07        22.72        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HD TCGA-XF-A8HE 
       46.98        14.24         1.84        33.14        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
       97.12         3.22        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
        2.10        13.74        10.82        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
       94.29         3.48        88.87        19.69        57.90        12.23 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 
       17.16        34.98        27.62        50.04        51.16        66.54 
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-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-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       19.50        14.96         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        36.43        28.41         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-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.34        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       29.79         1.84        18.41        16.14        17.62        15.62 
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-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        12.03        43.59        29.72         5.36 
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-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-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
       19.33         5.36         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
       10.85        12.66        10.65         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
        0.49         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
       15.78        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
        1.51        19.40        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        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-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P 
       16.67        16.54        17.62        37.05        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        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI 
        6.21         3.85        45.04         6.58         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       28.24        16.27        92.98         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       27.06        75.39        18.84         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       25.41        35.84        21.86        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       47.84         2.89         8.61        59.38        60.16        67.20 
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        29.49 
TCGA-ZF-AA5N 
        5.52 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.62               0.49 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            112.44             166.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            17.555             17.620 
[1] "0.6 - 112.4 (17.6)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.4"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         0        9        11       23
  10Q GAIN WILD-TYPE       2      120       129      112
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                 9                120
  STAGE III               11                129
  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  10
  10Q GAIN WILD-TYPE      110 174  48
D20V4, multiclass
          clus
vv         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1+T2               13                110
  T3                     21                174
  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
  10Q GAIN MUTATED    17  12  10   2
  10Q GAIN WILD-TYPE 219  35  65   6
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               17                219
  N1               12                 35
  N2               10                 65
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    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    10  34
  10Q GAIN WILD-TYPE  97 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     10   34
  10Q GAIN WILD-TYPE   97  267
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               10                 97
  MALE                 34                267
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    40   1
  10Q GAIN WILD-TYPE 324  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     40    1
  10Q GAIN WILD-TYPE  324   19
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                40                324
  YES                1                 19
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, continuous
D20V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       4                         1    35
  10Q GAIN WILD-TYPE    39                        21   292
D20V12, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                1                 21
  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"
D20V13, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  35
  10Q GAIN WILD-TYPE   8 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   35
  10Q GAIN WILD-TYPE    8  334
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               35                334
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    14  15
  11P GAIN WILD-TYPE 213 163
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                29                376 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                163 
$`11P GAIN MUTATED`
TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-DK-A3IV TCGA-E7-A7DV TCGA-FD-A3B6 
       25.94        12.92         4.90         9.67         1.22        33.04 
TCGA-FD-A5BT TCGA-FD-A62P TCGA-FD-A6TI TCGA-GV-A3JZ TCGA-GV-A40E TCGA-K4-A4AC 
       10.78         6.28         9.67        19.82         8.58         9.14 
TCGA-KQ-A41P TCGA-XF-A8HF TCGA-XF-A9SY TCGA-XF-AAMH TCGA-YF-AA3M TCGA-BL-A13J 
       35.97        97.12        21.04        11.31        13.64         2.66 
TCGA-DK-A3WX TCGA-E7-A5KF TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GU-A762 TCGA-GU-A766 
       10.55         0.66        20.71        15.91         7.63        15.78 
TCGA-GV-A3QI TCGA-LC-A66R TCGA-PQ-A6FI TCGA-UY-A9PB TCGA-UY-A9PF 
       36.49        15.32        12.23        29.56         3.85 

$`11P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C 
       26.14        14.89         8.35        20.48         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
        8.98        18.58        15.12        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       19.00        16.70       130.88        46.68        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 
       17.72        50.27        21.30        23.21        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       36.66        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        56.15        11.18        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        0.92         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       15.58        26.73        53.88         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       58.92        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        3.06         4.31        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G 
       10.92        32.78        32.98        20.28        27.35        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R 
       22.72         9.01        25.02         3.45         2.76        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       52.73        50.56        46.98        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SJ 
       86.83        51.32        97.45       125.49        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       10.82        54.90         7.63        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
        9.63        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         6.74         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        11.34        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
       13.58         8.15        20.81       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
        6.94        29.36        15.81        14.07         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
       11.31        18.97        20.05         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       21.34        19.10         8.48         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.58        21.07        13.48        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       17.62        37.05        22.68        76.01        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB 
        3.02       112.83        35.24        17.82         6.21        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        6.58         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
      110.60         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       75.39        18.84         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.66               0.49 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             97.12             166.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             12.23              17.88 
[1] "0.7 - 97.1 (12.2)"  "0.5 - 166.0 (17.9)"
[1] "hr=" "1.7"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         0       10         8       11
  11P GAIN WILD-TYPE       2      119       132      124
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                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
  11P GAIN MUTATED          8  13   6
  11P GAIN WILD-TYPE      115 182  52
D21V4, multiclass
          clus
vv         11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1+T2                8                115
  T3                     13                182
  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
  11P GAIN MUTATED    15   2   6   3
  11P GAIN WILD-TYPE 221  45  69   5
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               15                221
  N1                2                 45
  N2                6                 69
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     9   1
  11P GAIN WILD-TYPE 183  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      9    1
  11P GAIN WILD-TYPE  183   10
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                9                183
  1                1                 10
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  27
  11P GAIN WILD-TYPE 105 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   27
  11P GAIN WILD-TYPE  105  274
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                105
  MALE                 27                274
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    27   1
  11P GAIN WILD-TYPE 337  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     27    1
  11P GAIN WILD-TYPE  337   19
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                27                337
  YES                1                 19
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, continuous
D21V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       1                         0    27
  11P GAIN WILD-TYPE    42                        22   300
D21V12, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                 42
  BLACK OR AFRICAN AMERICAN                0                 22
  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"
D21V13, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  28
  11P GAIN WILD-TYPE   8 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   28
  11P GAIN WILD-TYPE    8  341
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               28                341
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    21  26
  11Q GAIN WILD-TYPE 206 152
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                47                358 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                26                152 
$`11Q GAIN MUTATED`
TCGA-4Z-AA84 TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-DK-A3X2 TCGA-E7-A7DV 
       15.12        25.94        12.92         4.90        17.98         1.22 
TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A62P 
       33.04        60.66        27.35        26.73        10.78         6.28 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-AA3D TCGA-GV-A3QF TCGA-GV-A40E 
        3.06         9.67        31.07        70.32        20.28         8.58 
TCGA-K4-A4AC TCGA-KQ-A41P TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HF TCGA-XF-A9SY 
        9.14        35.97         1.84        33.14        97.12        21.04 
TCGA-XF-AAMH TCGA-YF-AA3M TCGA-4Z-AA80 TCGA-BL-A13J TCGA-C4-A0F6 TCGA-DK-A1A3 
       11.31        13.64         0.62         2.66        23.01        21.86 
TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA76 TCGA-E7-A5KF TCGA-G2-AA3F TCGA-GC-A3I6 
        8.15        10.55        12.03         0.66        29.36        20.71 
TCGA-GC-A3RC TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-LC-A66R TCGA-PQ-A6FI 
       15.91         7.63        15.78         4.73        15.32        12.23 
TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PF TCGA-XF-AAMX TCGA-ZF-AA51 
       22.68         3.02         3.85         6.77        56.35 

$`11Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
       14.89         8.35        20.48         9.96        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       18.58        15.12        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       16.70       130.88        46.68        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV 
       50.27        21.30        23.21         9.67        66.05        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       56.15        11.18        20.32        15.35        25.58         0.92 
TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        4.01        24.30        23.41        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BX 
       19.79        12.85         3.62        15.58        53.88         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        8.25        18.08        58.92        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
       12.69        12.36         4.31        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       17.62        21.40        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
       32.78        32.98        19.82        27.35        19.07        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N 
        9.01        25.02         3.45         2.76        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD 
       50.56        46.98        14.24        86.83        51.32        97.45 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
      125.49        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        12.76        11.90        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        13.74        10.82        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       86.30        18.58         3.88         9.63        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         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-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42        40.08         7.33         6.74         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-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       36.43        28.41         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-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.34        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
       29.79         1.84        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       13.58        20.81       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        43.59        38.83        29.72         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 
       22.16         2.24        16.70         0.56        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3OO 
       59.31         7.23        20.12        66.02         6.94        15.81 
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        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 
        3.12        20.98         2.20        11.31        18.97        20.05 
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-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
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-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       11.80        44.38         1.15        15.58        21.07        13.48 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O 
       16.67        16.54        38.99        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        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        6.21        45.04         6.58         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       16.27        92.98       110.60         2.96         8.32        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       27.06        75.39        18.84         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       59.38        60.16        67.20        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.62               0.49 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             97.12             166.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.64              17.85 
[1] "0.6 - 97.1 (13.6)"  "0.5 - 166.0 (17.9)"
[1] "hr=" "1.7"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         0       15         9       23
  11Q GAIN WILD-TYPE       2      114       131      112
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                15                114
  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         14  22   9
  11Q GAIN WILD-TYPE      109 173  49
D22V4, multiclass
          clus
vv         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1+T2               14                109
  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  16   2
  11Q GAIN WILD-TYPE 215  42  59   6
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               21                215
  N1                5                 42
  N2               16                 59
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    18   2
  11Q GAIN WILD-TYPE 174   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     18    2
  11Q GAIN WILD-TYPE  174    9
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               18                174
  1                2                  9
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     7  40
  11Q GAIN WILD-TYPE 100 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7   40
  11Q GAIN WILD-TYPE  100  261
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                7                100
  MALE                 40                261
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    41   1
  11Q GAIN WILD-TYPE 323  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     41    1
  11Q GAIN WILD-TYPE  323   19
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                41                323
  YES                1                 19
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, continuous
D22V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       2                         2    41
  11Q GAIN WILD-TYPE    41                        20   286
D22V12, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    2                 41
  BLACK OR AFRICAN AMERICAN                2                 20
  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"
D22V13, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  43
  11Q GAIN WILD-TYPE   8 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   43
  11Q GAIN WILD-TYPE    8  326
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               43                326
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    62  54
  12P GAIN WILD-TYPE 165 124
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               116                289 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                54                124 
$`12P GAIN MUTATED`
TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CU-A0YN 
       15.12        26.14        20.48        25.94         9.96        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 
        4.90        15.12        50.27        66.05        64.18        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-DK-AA75 TCGA-FD-A3B6 TCGA-FD-A3NA 
       15.68        36.66       166.03        11.18        33.04        60.66 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A62P TCGA-FD-A6TB 
       12.85        27.35        53.88         5.69         6.28        18.81 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GV-A3JZ TCGA-GV-A3QK 
       31.07        11.08        17.62        21.40        19.82        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AC TCGA-KQ-A41P 
        8.58        19.07         9.01         3.45         9.14        35.97 
TCGA-XF-A9SK TCGA-XF-A9SV TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 
       15.98        12.76         7.63        98.99        44.32        86.30 
TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-2F-A9KO TCGA-2F-A9KP 
       18.58        13.64        21.11        30.28        24.13        11.97 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
        0.62        41.75        10.22        40.08         2.66         6.74 
TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB 
       19.04        17.88         5.06         5.06         8.25        16.18 
TCGA-BT-A42E TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY 
       36.43        12.13        13.08        12.00        11.34        11.34 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6T 
       21.86        66.41         8.15        10.55        15.02        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME 
       19.00        15.35        12.03        22.16         0.56        24.03 
TCGA-FD-A3B3 TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62S TCGA-G2-A2EO TCGA-G2-AA3B 
       32.02         5.36        27.45        13.35        59.31        66.02 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GU-A762 TCGA-GU-AATQ 
       20.71        15.81        14.07        13.91         7.63         7.00 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        8.48        36.49        38.60        64.01        12.16        21.24 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78O 
       11.70         1.81        16.27        13.48        38.99        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PE TCGA-XF-A9SI TCGA-XF-A9SU 
       78.25        69.34        35.24         6.21        79.66         5.98 
TCGA-XF-AAMT TCGA-XF-AAN5 TCGA-ZF-A9R1 TCGA-ZF-A9RD TCGA-ZF-AA4N TCGA-ZF-AA4V 
        2.96        75.39        25.41        13.41         2.89        59.38 
TCGA-ZF-AA54 TCGA-GU-AATO 
       19.40        10.65 

$`12P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T 
      108.95        16.27        16.77        33.83        12.39        14.89 
TCGA-BT-A20W TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A3KJ TCGA-CU-A72E 
        8.35        28.70         8.98        18.58        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
        2.14        19.00        16.70       130.88        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 
        8.22        17.72        21.30        23.21         9.67        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       53.29        76.60        50.70        38.24        52.01       165.73 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        13.64        56.15        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        0.92         1.22         4.01        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       29.16        46.78        19.79         3.62        15.58        26.73 
TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TC 
       10.78         8.25        18.08        58.92        62.86         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF 
       12.69        12.36         3.06         4.31         9.67        17.23 
TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       33.01        70.32        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB 
       32.78        32.98        20.28        22.72        25.02         2.76 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       27.68        52.73        50.56        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       33.14        86.83        51.32        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW 
       15.35         3.22        34.45        14.93         4.21        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        10.82        11.31        54.90        71.57        91.73 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       30.94        61.45         3.88         9.63        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KQ 
       88.87        34.06        19.69        57.90        12.23        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KI 
       27.62        50.04        51.16        66.54        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20Q 
       17.42         7.33         6.58        13.15        12.16        19.50 
TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 
       14.96        17.16         4.67        17.56        28.41         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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       13.12        12.10        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        1.84        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW 
       17.95         7.79       142.78         4.80        13.58        20.81 
TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
      163.30        13.58        43.59        38.83        29.72         5.36 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
        2.24        16.70         0.66        26.96        26.24         4.24 
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-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.09        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.70         7.10         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A4ZW 
        7.23        20.12         6.94        29.36        15.91         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV 
       11.31        18.97        20.05        15.78         4.73        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A5RH TCGA-K4-A5RJ 
       21.34        19.10         1.51        19.40         9.07        17.72 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       15.42        11.80        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L 
       21.07        12.23        16.67        16.54        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
       22.68         3.02       112.83        29.56        17.82         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       45.04         6.58         1.87        17.88        48.62        64.80 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
       66.41        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A89H TCGA-YC-A9TC 
        8.32         6.77        56.48        27.06        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       11.97        22.36        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W 
       64.08        58.72        47.84        20.22         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       67.20        56.35        35.41         8.52        54.21        29.49 
TCGA-ZF-AA5N 
        5.52 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.56               0.49 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            166.03             165.73 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            16.945             17.720 
[1] "0.6 - 166.0 (16.9)" "0.5 - 165.7 (17.7)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         1       42        34       38
  12P GAIN WILD-TYPE       1       87       106       97
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  1                  1
  STAGE II                42                 87
  STAGE III               34                106
  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
  12P GAIN MUTATED         37  56  13
  12P GAIN WILD-TYPE       86 139  45
D23V4, multiclass
          clus
vv         12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1+T2               37                 86
  T3                     56                139
  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
  12P GAIN MUTATED    66  16  20   3
  12P GAIN WILD-TYPE 170  31  55   5
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               66                170
  N1               16                 31
  N2               20                 55
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    57   3
  12P GAIN WILD-TYPE 135   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     57    3
  12P GAIN WILD-TYPE  135    8
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               57                135
  1                3                  8
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    32  84
  12P GAIN WILD-TYPE  75 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     32   84
  12P GAIN WILD-TYPE   75  217
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               32                 75
  MALE                 84                217
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   108   5
  12P GAIN WILD-TYPE 256  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    108    5
  12P GAIN WILD-TYPE  256   15
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO               108                256
  YES                5                 15
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, continuous
D23V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED      11                         5    94
  12P GAIN WILD-TYPE    32                        17   233
D23V12, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                   11                 32
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                   94                233
[1] 3 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     3 103
  12P GAIN WILD-TYPE   6 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3  103
  12P GAIN WILD-TYPE    6  266
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              103                266
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    53  38
  12Q GAIN WILD-TYPE 174 140
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                91                314 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                38                140 
$`12Q GAIN MUTATED`
TCGA-4Z-AA84 TCGA-BT-A3PK TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A1AC 
       15.12         9.96         4.90        15.12         2.14       130.88 
TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-AA6S TCGA-DK-AA71 
       50.27        66.05        64.18        67.36       166.03        13.64 
TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BX TCGA-FD-A62P TCGA-FJ-A3Z7 
       60.66        27.35        15.58         5.69         6.28        31.07 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GV-A3QK TCGA-GV-A40E TCGA-K4-A3WU TCGA-KQ-A41P 
       17.62        21.40        27.35         8.58         3.45        35.97 
TCGA-XF-A9SV TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 
       12.76         7.63        98.99        44.32        86.30        18.58 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-2F-A9KO TCGA-2F-A9KP TCGA-4Z-AA80 
       13.64        21.11        30.28        24.13        11.97         0.62 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20R 
       40.08         2.66         6.74        19.04        17.88         5.06 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A42E TCGA-CF-A3MF TCGA-CF-A3MG 
        5.06         8.25        16.18        36.43        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A5W6 TCGA-DK-A1A3 
       13.08        12.00        11.34        11.34         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       66.41        10.55        15.02        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62S 
       12.03         0.56        24.03         5.36        27.45        13.35 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-GC-A3I6 TCGA-GC-A6I3 TCGA-GV-A3QH TCGA-GV-A3QI 
       61.94        59.31        20.71        13.91         8.48        36.49 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-MV-A51V 
       38.60        64.01        11.70         1.81        16.27        13.48 
TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PE 
       38.99        76.01        78.25        69.34        35.24         6.21 
TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAMT TCGA-ZF-A9R1 TCGA-ZF-A9RN TCGA-ZF-AA4V 
       79.66         5.98         2.96        25.41        20.22        59.38 
TCGA-GU-AATO 
       10.65 

$`12Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ 
       14.89         8.35        20.48        25.94        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB 
       18.58        12.92        18.48        13.58        19.00        16.70 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       46.68        87.32         8.22        17.72        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
        9.67        17.98        53.29        76.60        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 
       36.66        38.24        52.01       165.73        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       33.04         4.01        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        19.79        12.85         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB 
       10.78         8.25        18.08        58.92        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         3.06         4.31         9.67 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
       17.23        11.08        33.01        70.32        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC 
       19.07        22.72         9.01        25.02         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       27.68        52.73        50.56        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       33.14        86.83        51.32        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       15.35         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
        2.10        13.74        10.82        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9RC 
       91.73        30.94        61.45         3.88         9.63        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62        50.04        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0S7 
       10.22        47.80         2.50        17.42         7.33         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A3PH 
       13.15        12.16        19.50        14.96        17.16         4.67 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       17.56        28.41         1.94        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.97        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM 
       12.62        12.26        13.12        12.10        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
        5.19        29.79        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-E5-A2PC TCGA-E5-A4U1 
        8.15        20.81       163.30        13.58        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       29.72         5.36        22.16         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.96        26.24         4.24        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A62O 
       22.98        14.96        20.91        19.33         2.70         7.10 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       48.00        15.95        26.93         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW 
        6.94        29.36        15.81        15.91        14.07         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.00        14.27        21.34        19.10         1.51        19.40 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO 
       12.16        21.24         9.07        17.72        15.42        11.80 
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-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OC 
       16.67        16.54        17.62        37.05        22.68         3.02 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
      112.83        29.56        17.82         3.85        45.04         6.58 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX 
        1.87        17.88        48.62        64.80        66.41        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX 
       28.24        16.27        92.98       110.60         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       22.36        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       64.08        58.72        47.84         2.89         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       29.49         5.52 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.56               0.49 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            166.03             165.73 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             16.27              17.72 
[1] "0.6 - 166.0 (16.3)" "0.5 - 165.7 (17.7)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         1       35        26       28
  12Q GAIN WILD-TYPE       1       94       114      107
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  1                  1
  STAGE II                35                 94
  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         31  39  12
  12Q GAIN WILD-TYPE       92 156  46
D24V4, multiclass
          clus
vv         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1+T2               31                 92
  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
  12Q GAIN MUTATED    54  11  17   1
  12Q GAIN WILD-TYPE 182  36  58   7
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               54                182
  N1               11                 36
  N2               17                 58
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    26  65
  12Q GAIN WILD-TYPE  81 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     26   65
  12Q GAIN WILD-TYPE   81  236
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               26                 81
  MALE                 65                236
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    85   5
  12Q GAIN WILD-TYPE 279  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     85    5
  12Q GAIN WILD-TYPE  279   15
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                85                279
  YES                5                 15
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, continuous
D24V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED      11                         4    73
  12Q GAIN WILD-TYPE    32                        18   254
D24V12, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                   11                 32
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   73                254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  83
  12Q GAIN WILD-TYPE   7 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   83
  12Q GAIN WILD-TYPE    7  286
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               83                286
[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 173 133
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                99                306 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                45                133 
$`13Q GAIN MUTATED`
TCGA-2F-A9KT TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YR 
      108.95        20.48        25.94         8.98        12.92        15.12 
TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 
       46.68        50.27        23.21        66.05        17.98        67.36 
TCGA-DK-AA6L TCGA-DK-AA6S TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3SM 
       38.24       166.03        25.58         0.92        33.04        17.98 
TCGA-FD-A3SQ TCGA-FD-A43X TCGA-FD-A5BT TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       46.78         3.62        10.78        12.36         3.06         4.31 
TCGA-FT-A61P TCGA-G2-AA3D TCGA-GC-A3WC TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       11.08        70.32        17.75        19.82        20.28        27.35 
TCGA-K4-A54R TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A8HD 
       27.68        35.97        14.24         1.84        51.32        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-AAMQ 
       97.12        15.35         3.22        15.98        14.93        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-4Z-AA81 
       91.73        98.99        61.45        19.69        24.13        41.75 
TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20Q TCGA-BT-A20U 
       47.80         6.74         6.58        19.04        19.50        14.96 
TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A8HX TCGA-CU-A3QU TCGA-CU-A3YL 
       12.56        12.13        12.16        11.34         5.19        29.79 
TCGA-DK-A3IL TCGA-DK-AA6P TCGA-DK-AA6U TCGA-E5-A2PC TCGA-E7-A6ME TCGA-E7-A7PW 
       13.58        15.02        19.00        43.59        24.03        13.68 
TCGA-E7-A97Q TCGA-FD-A62O TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-AA3B 
        8.09         7.10        10.65        61.94        15.95        66.02 
TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A767 TCGA-GU-AATQ 
       15.81         0.49         2.10        20.98         4.73         7.00 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-AAQO 
       19.10         8.48        19.40        12.16         9.07        11.80 
TCGA-LC-A66R TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       15.32        13.48        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-XF-AAN0 TCGA-ZF-A9R0 
       76.01        78.25       112.83        35.24        56.48        22.36 
TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-GU-AATO 
       67.20         8.52        10.65 

$`13Q GAIN WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YO 
       14.89         8.35         9.96        28.70        18.58         4.90 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6AV 
       87.32         8.22        17.72        21.30         9.67        64.18 
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-AA6R TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      165.73        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       15.35         1.22         4.01        60.66        24.30        23.41 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR 
       29.16        19.79        12.85        27.35        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       53.88         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 
       62.86        18.81         6.15        12.69         9.67        31.07 
TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS 
       17.23        33.01        17.62        21.40        19.13        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       10.92        32.78        32.98         8.58        19.07        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N 
        9.01        25.02         3.45         2.76         9.14        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HE TCGA-XF-A9SM 
       50.56        46.98        33.14        86.83       125.49        34.45 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 
       54.90         7.63        44.32        30.94        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP 
        3.48        88.87        34.06        57.90        12.23        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62        50.04         0.62        51.16        66.54 
TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22         2.50        17.42        40.08         7.33         2.66 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X 
       13.15        12.16        17.88         5.06         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH 
        1.94        23.01        12.79        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-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
        8.15        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       15.35        12.03        38.83        29.72         5.36        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-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        4.24        24.66        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
        5.36        27.45         2.70        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
       12.66         8.94         3.25        48.00        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC 
        7.23        20.12         6.94        29.36        20.71        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 
       14.07         8.94        13.91        26.70         3.12         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV 
       11.31        18.97         7.63        20.05        15.78        14.27 
TCGA-GV-A3JW TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV 
       21.34        36.49         1.51        38.60        64.01        21.24 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R 
       11.70        17.72         1.81        15.42        16.27        44.38 
TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
        1.15        15.58        21.07        12.23        16.67        16.54 
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-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       45.04         6.58         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 
       92.98       110.60         2.96         8.32         6.77        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39        18.84         0.66        11.97        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
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        29.49         5.52 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.49               0.56 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            166.03             165.73 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            19.040             17.195 
[1] "0.5 - 166.0 (19.0)" "0.6 - 165.7 (17.2)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         0       29        32       39
  13Q GAIN WILD-TYPE       2      100       108       96
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                29                100
  STAGE III               32                108
  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
  13Q GAIN MUTATED         27  49  14
  13Q GAIN WILD-TYPE       96 146  44
D25V4, multiclass
          clus
vv         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1+T2               27                 96
  T3                     49                146
  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
  13Q GAIN MUTATED    55   8  25   5
  13Q GAIN WILD-TYPE 181  39  50   3
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               55                181
  N1                8                 39
  N2               25                 50
  N3                5                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    45   5
  13Q GAIN WILD-TYPE 147   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     45    5
  13Q GAIN WILD-TYPE  147    6
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               45                147
  1                5                  6
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    23  77
  13Q GAIN WILD-TYPE  84 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     23   77
  13Q GAIN WILD-TYPE   84  224
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               23                 84
  MALE                 77                224
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    88   4
  13Q GAIN WILD-TYPE 276  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     88    4
  13Q GAIN WILD-TYPE  276   16
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                88                276
  YES                4                 16
[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  33
  14Q GAIN WILD-TYPE 203 145
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                57                348 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                33                145 
$`14Q GAIN MUTATED`
TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A3IN TCGA-DK-A3IT 
       12.39        26.14         8.98        12.92         8.22        21.30 
TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA74 TCGA-FD-A3B7 TCGA-FD-A5BT TCGA-FD-A6TD 
       36.66       165.73        56.15         4.01        10.78        12.69 
TCGA-FD-A6TE TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GU-A42P TCGA-K4-A4AC TCGA-KQ-A41O 
       12.36        21.40        24.92        10.92         9.14        50.56 
TCGA-XF-A8HG TCGA-XF-A9SP TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMQ TCGA-ZF-AA4R 
       15.35        14.93         2.24        10.82        71.57        34.06 
TCGA-4Z-AA7R TCGA-BT-A0S7 TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-DK-A3WX TCGA-E5-A2PC 
       17.16         6.58         1.94        23.01        10.55        43.59 
TCGA-FD-A3B3 TCGA-FD-A3N5 TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FJ-A3ZE 
       32.02        22.52        27.45         7.10        13.35        10.65 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-GC-A3I6 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-AATQ 
       26.93        59.31        20.71        20.98         2.20         7.00 
TCGA-GV-A3QH TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-LT-A5Z6 TCGA-PQ-A6FN 
        8.48        21.24        11.70         1.81        15.58        16.67 
TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A8HB TCGA-XF-AAMT TCGA-ZF-A9R0 TCGA-ZF-A9RD 
       76.01       112.83        45.04         2.96        22.36        13.41 
TCGA-ZF-A9RG TCGA-ZF-AA5H TCGA-GU-AATO 
       58.72        29.49        10.65 

$`14Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20T 
      108.95        16.27        16.77        15.12        33.83        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A9FL 
        8.35        20.48        25.94         9.96        28.70        18.58 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
        4.90        15.12        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS 
       16.70       130.88        46.68        87.32        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M 
       76.60        67.36        15.68        50.70        38.24        52.01 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
      166.03        13.64        13.64        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       25.58         0.92         1.22        33.04        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-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BX 
       27.35         3.62        15.58        26.73        53.88         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.15         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
       11.08        33.01        17.62        70.32        19.13        17.75 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       27.68        52.73        35.97        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       33.14        86.83        51.32        97.45       125.49        97.12 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
        3.22        15.98        34.45         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       21.04        26.27        18.90        66.64         2.10        13.74 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       11.31        54.90         7.63        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
       13.64        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W 
      104.65         8.35        44.94        16.83        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS 
        4.67        17.56        36.43        28.41        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-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
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-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY 
      142.78         4.80        13.58         8.15        20.81       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
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-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-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO 
        8.09        16.77         8.94        12.62        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A62N TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE 
        2.70         2.27        10.85        12.66         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       61.94        48.00        15.95         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW 
        6.94        29.36        15.81        15.91        14.07         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42Q 
        8.94        13.91        26.70         2.10         3.12        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV 
       18.97         7.63        20.05        15.78         4.73        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       21.34        19.10        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
       64.01        12.16         9.07        17.72        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V 
       11.80        44.38         1.15        15.32        21.07        13.48 
TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       12.23        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       78.25        69.34         3.02        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        6.21         3.85         6.58         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       16.27        92.98       110.60         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        11.97        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RM 
       31.20        35.84        21.86        28.41        64.08        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        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       56.35        35.41        19.40         8.52        54.21         5.52 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.81               0.49 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            165.73             166.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            15.580             17.735 
[1] "1.8 - 165.7 (15.6)" "0.5 - 166.0 (17.7)"
[1] "hr=" "1.5"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         0       14        25       18
  14Q GAIN WILD-TYPE       2      115       115      117
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                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
  14Q GAIN MUTATED         10  34   7
  14Q GAIN WILD-TYPE      113 161  51
D26V4, multiclass
          clus
vv         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1+T2               10                113
  T3                     34                161
  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   8   1
  14Q GAIN WILD-TYPE 201  39  67   7
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               35                201
  N1                8                 39
  N2                8                 67
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    17   2
  14Q GAIN WILD-TYPE 175   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     17    2
  14Q GAIN WILD-TYPE  175    9
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               17                175
  1                2                  9
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    22  35
  14Q GAIN WILD-TYPE  85 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     22   35
  14Q GAIN WILD-TYPE   85  266
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               22                 85
  MALE                 35                266
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    52   2
  14Q GAIN WILD-TYPE 312  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     52    2
  14Q GAIN WILD-TYPE  312   18
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                52                312
  YES                2                 18
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, continuous
D26V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         5    46
  14Q GAIN WILD-TYPE    43                        17   281
D26V12, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                 43
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                   46                281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  49
  14Q GAIN WILD-TYPE   7 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   49
  14Q GAIN WILD-TYPE    7  320
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               49                320
[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 211 161
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                372 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                17                161 
$`15Q GAIN MUTATED`
TCGA-4Z-AA89 TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A6B1 TCGA-E5-A4TZ 
       33.83         2.14        46.68        50.27        67.36        15.35 
TCGA-FD-A43X TCGA-FD-A6TG TCGA-GC-A3BM TCGA-GU-AATP TCGA-S5-A6DX TCGA-UY-A9PH 
        3.62         3.06        21.40        32.98         1.84        51.32 
TCGA-XF-AAMQ TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-ZF-A9RE TCGA-4Z-AA7R TCGA-BT-A20Q 
       71.57        44.32        30.94         3.48        17.16        19.50 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A3MH TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A3YL 
       28.41        23.01        13.08        12.00        11.34        29.79 
TCGA-CU-A5W6 TCGA-DK-A3WX TCGA-DK-AA6Q TCGA-E7-A6MD TCGA-FD-A43U TCGA-FJ-A3ZE 
        1.84        10.55        13.58         4.24        20.91        10.65 
TCGA-G2-A2EO TCGA-GC-A3I6 TCGA-UY-A8OB 
       59.31        20.71        69.34 

$`15Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        15.12        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN 
       13.58        19.00        16.70       130.88        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       17.72        21.30        23.21         9.67        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-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       56.15        11.18        20.32        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y 
       29.16        46.78        19.79        12.85        27.35        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
       12.36         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       33.01        17.62        70.32        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       10.92        32.78        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       14.24        33.14        86.83        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       15.35         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
        7.63        91.73        98.99        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       88.87        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       12.16        17.88         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 
       17.16        16.18         4.67        17.56        36.43         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI 
       12.79        12.56        13.97        12.59        12.13        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-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       13.12        12.10        11.34        11.87        13.08         5.19 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
        8.15        20.81       163.30        15.02        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.35        12.03        43.59        38.83        29.72         5.36 
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-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       26.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       14.96        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE 
       13.35         2.27        10.85        12.66         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-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       66.02         6.94        29.36        15.81        15.91        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
        0.49         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48        36.49         1.51        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       12.16        21.24         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       15.42        16.27        11.80        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.58        21.07        13.48        12.23        16.67        16.54 
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-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
        3.02       112.83        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        3.85        45.04         6.58         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
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-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.84               0.49 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             71.57             166.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             20.71              17.62 
[1] "1.8 - 71.6 (20.7)"  "0.5 - 166.0 (17.6)"
[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 216  43  67   6
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               20                216
  N1                4                 43
  N2                8                 67
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    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  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     29    3
  15Q GAIN WILD-TYPE  335   17
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                29                335
  YES                3                 17
[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    36  38
  16P GAIN WILD-TYPE 191 140
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                74                331 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                140 
$`16P GAIN MUTATED`
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV 
       28.70         8.98         8.22        50.27        21.30         9.67 
TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-AA6S TCGA-DK-AA75 TCGA-FD-A3SJ TCGA-FD-A5BY 
       66.05        15.68       166.03        11.18        24.30         8.25 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GU-AATP TCGA-HQ-A5ND 
        3.06         9.67        70.32        21.40        32.98         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH 
       25.02         3.45         2.76        14.24         1.84        51.32 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAML 
        3.22        15.98        34.45        66.64        10.82         7.63 
TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-ZF-A9R2 TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA87 
       91.73        44.32        21.11        27.62         0.62        47.80 
TCGA-5N-A9KI TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        2.50         2.66         6.58         5.06         8.25        17.16 
TCGA-CF-A47X TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC 
       12.62         7.79        13.58        19.00        15.35        43.59 
TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A97Q TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-FT-A3EE 
       22.16        24.03         8.09         2.27        10.65         3.25 
TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GU-A762 TCGA-GV-A3JV TCGA-H4-A2HQ 
       59.31        66.02        20.71         7.63        14.27        19.40 
TCGA-HQ-A2OF TCGA-K4-A83P TCGA-LC-A66R TCGA-SY-A9G5 TCGA-UY-A78M TCGA-XF-A9SU 
       64.01        16.27        15.32        38.99        22.68         5.98 
TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMX TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-AA4V 
       28.24       110.60         6.77        22.36        13.41        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA5H 
       60.16        29.49 

$`16P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
       18.58        12.92         4.90        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
        2.14        19.00        16.70       130.88        46.68        87.32 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       17.72        23.21        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       67.36        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        13.64        56.15        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL 
        0.92         1.22        33.04         4.01        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
        3.62        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
       12.69        12.36         4.31        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       33.01        17.62        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.78        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
       22.72         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       46.98        33.14        86.83        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       15.35        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH 
       26.27        18.90         2.24         2.10        13.74        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       54.90        71.57        98.99        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       18.58         3.88         9.63        13.64        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.83        17.16        34.98        50.04        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       66.54        10.22        17.42        40.08         7.33         6.74 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       14.96        16.18         4.67        17.56        36.43        28.41 
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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW 
       15.62        17.95       142.78         4.80         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 
       10.55       163.30        15.02        13.58        18.81        12.03 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        29.72         5.36         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7PW 
        0.66        26.96        26.24         4.24        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        15.32        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 
        2.70         7.10        13.35        10.85        12.66         8.94 
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-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW 
        6.94        29.36        15.81        15.91        14.07         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
        2.20        11.31        18.97        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
        7.00        21.34        19.10         8.48        36.49         1.51 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       38.60        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 
        1.81        15.42        11.80        44.38         1.15        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K 
       21.07        13.48        12.23        16.67        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        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 
       35.24        29.56        17.82         6.21         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        6.58         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW 
       66.41        23.64        16.27        92.98         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF 
       25.41        31.20        35.84        21.86        28.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X 
       58.72        47.84        20.22         2.89         8.61        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       56.35        35.41        19.40         8.52        54.21         5.52 
TCGA-GU-AATO 
       10.65 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.62               0.49 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            166.03             165.73 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            16.125             17.720 
[1] "0.6 - 166.0 (16.1)" "0.5 - 165.7 (17.7)"
[1] "hr=" "1.3"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         0       16        26       33
  16P GAIN WILD-TYPE       2      113       114      102
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                33                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  16P GAIN MUTATED         16  34  19
  16P GAIN WILD-TYPE      107 161  39
D28V4, multiclass
          clus
vv         16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1+T2               16                107
  T3                     34                161
  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
  16P GAIN MUTATED    37  10  19   3
  16P GAIN WILD-TYPE 199  37  56   5
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               37                199
  N1               10                 37
  N2               19                 56
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    36   4
  16P GAIN WILD-TYPE 156   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     36    4
  16P GAIN WILD-TYPE  156    7
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               36                156
  1                4                  7
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    22  53
  16P GAIN WILD-TYPE  85 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     22   53
  16P GAIN WILD-TYPE   85  248
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               22                 85
  MALE                 53                248
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    69   3
  16P GAIN WILD-TYPE 295  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     69    3
  16P GAIN WILD-TYPE  295   17
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                69                295
  YES                3                 17
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, continuous
D28V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       4                         4    64
  16P GAIN WILD-TYPE    39                        18   263
D28V12, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   64                263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  68
  16P GAIN WILD-TYPE   8 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   68
  16P GAIN WILD-TYPE    8  301
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               68                301
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    45  36
  16Q GAIN WILD-TYPE 182 142
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                81                324 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                36                142 
$`16Q GAIN MUTATED`
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A3KJ TCGA-DK-A3IN TCGA-DK-A3IS 
       25.94        28.70         8.98        18.48         8.22        50.27 
TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-AA6S TCGA-DK-AA75 TCGA-FD-A43P 
       21.30        66.05        15.68       166.03        11.18        27.35 
TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TG TCGA-FD-A6TI TCGA-G2-A3VY 
       15.58         8.25         6.28         3.06         9.67        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GU-AATP TCGA-HQ-A5ND TCGA-K4-A3WS 
       70.32        21.40        24.92        32.98         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A9SK 
        3.45         2.76        14.24         1.84        51.32        15.98 
TCGA-XF-A9SM TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9R2 
       34.45        10.82        91.73        98.99        44.32        21.11 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A13J TCGA-BT-A0S7 
       27.62         0.62        47.80         2.50         2.66         6.58 
TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-CF-A47X TCGA-DK-A2I2 
        5.06         5.06         8.25        17.16        12.62         7.79 
TCGA-DK-A3IL TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A6ME TCGA-E7-A97Q 
       13.58        19.00        15.35        43.59        24.03         8.09 
TCGA-FD-A3B3 TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO 
       32.02         2.27        10.85        10.65         3.25        59.31 
TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GU-A762 
       66.02        20.71         8.94        26.70        20.98         7.63 
TCGA-GV-A3JW TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A6MB TCGA-LC-A66R TCGA-SY-A9G5 
       21.34        19.40        64.01        15.42        15.32        38.99 
TCGA-UY-A78M TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SU TCGA-ZF-A9R0 TCGA-ZF-A9RD 
       22.68         6.21        48.62         5.98        22.36        13.41 
TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA5H 
       60.16        19.40        29.49 

$`16Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-CF-A9FL 
       26.14        14.89         8.35        20.48         9.96        18.58 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       12.92         4.90        15.12        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IU 
       16.70       130.88        46.68        87.32        17.72        23.21 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W 
       50.70        36.66        38.24        52.01       165.73        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       13.64        56.15        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X 
       17.98        29.16        46.78        19.79        12.85         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 
       26.73        53.88        10.78         5.69        18.08        58.92 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
       62.86        18.81         6.15        12.69        12.36         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3RB TCGA-GC-A3WC 
       31.07        17.23        11.08        33.01        19.13        17.75 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       10.92        32.78        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
       19.07        22.72         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE 
       35.97        46.98        33.14        86.83        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
       97.12        15.35         3.22        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
        2.10        13.74        11.31        54.90         7.63        71.57 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       13.64        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KM 
       50.04        41.75        51.16        66.54        10.22        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
       40.08         7.33         6.74        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       17.88        19.50        14.96        16.18         4.67        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-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-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.34        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       29.79         1.84        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK 
       16.14        17.62        15.62        17.95       142.78         4.80 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       18.81        12.03        38.83        29.72         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        4.24        24.66        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       14.37        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FJ-A3Z9 
        5.36        27.45         2.70         7.10        13.35        12.66 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        8.94        61.94        48.00        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12         6.94        29.36        15.81        15.91        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
        0.49        13.91         2.10         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
       18.97        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE 
       19.10         8.48        36.49         1.51        38.60        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
       21.24         9.07        11.70        17.72         1.81        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       11.80        44.38         1.15        15.58        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O 
       12.23        16.67        16.54        17.62        37.05        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        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI 
       17.82         3.85        45.04         6.58         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        79.66        66.41        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        11.97        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG 
       31.20        35.84        21.86        28.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
       47.84        20.22         2.89         8.61        59.38        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       56.35        35.41         8.52        54.21         5.52        10.65 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.62               0.49 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            166.03             165.73 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             17.62              17.67 
[1] "0.6 - 166.0 (17.6)" "0.5 - 165.7 (17.7)"
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         0       20        30       32
  16Q GAIN WILD-TYPE       2      109       110      103
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                20                109
  STAGE III               30                110
  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
  16Q GAIN MUTATED         19  38  18
  16Q GAIN WILD-TYPE      104 157  40
D29V4, multiclass
          clus
vv         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1+T2               19                104
  T3                     38                157
  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
  16Q GAIN MUTATED    43  10  18   3
  16Q GAIN WILD-TYPE 193  37  57   5
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               43                193
  N1               10                 37
  N2               18                 57
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    36   4
  16Q GAIN WILD-TYPE 156   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     36    4
  16Q GAIN WILD-TYPE  156    7
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               36                156
  1                4                  7
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    25  57
  16Q GAIN WILD-TYPE  82 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     25   57
  16Q GAIN WILD-TYPE   82  244
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               25                 82
  MALE                 57                244
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    73   4
  16Q GAIN WILD-TYPE 291  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     73    4
  16Q GAIN WILD-TYPE  291   16
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                73                291
  YES                4                 16
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, continuous
D29V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       4                         4    70
  16Q GAIN WILD-TYPE    39                        18   257
D29V12, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   70                257
[1] 3 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  75
  16Q GAIN WILD-TYPE   8 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   75
  16Q GAIN WILD-TYPE    8  294
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               75                294
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    30  26
  17P GAIN WILD-TYPE 197 152
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                56                349 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                26                152 
$`17P GAIN MUTATED`
TCGA-4Z-AA84 TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ 
       15.12         8.35        20.48        25.94        28.70         8.98 
TCGA-CU-A0YR TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA75 TCGA-FD-A3B7 TCGA-FD-A5BT 
       15.12        67.36        36.66        11.18         4.01        10.78 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-K4-A3WU TCGA-UY-A78N TCGA-XF-A9T0 
       12.36         4.31        31.07         3.45        86.83        26.27 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-2F-A9KP TCGA-4Z-AA81 
        7.63        71.57        30.28        94.29        11.97        41.75 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       10.22        47.80        40.08         2.66         6.74         6.58 
TCGA-BT-A20R TCGA-BT-A20U TCGA-CF-A3MF TCGA-CF-A8HY TCGA-DK-A3IM TCGA-DK-AA6P 
        5.06        14.96        12.59        11.34         8.15        15.02 
TCGA-E7-A5KE TCGA-FD-A3SP TCGA-FD-A6TF TCGA-FT-A3EE TCGA-G2-AA3F TCGA-GV-A3JV 
        0.56        25.74         2.27         3.25        29.36        14.27 
TCGA-GV-A3QH TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-LC-A66R TCGA-MV-A51V 
        8.48        38.60        21.24         1.81        15.32        13.48 
TCGA-UY-A8OB TCGA-UY-A9PB TCGA-XF-A8HI TCGA-ZF-A9RD TCGA-ZF-AA4V TCGA-ZF-AA4X 
       69.34        29.56        17.88        13.41        59.38        67.20 
TCGA-ZF-AA52 TCGA-ZF-AA5H 
       35.41        29.49 

$`17P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
       14.89         9.96        18.58        12.92         4.90        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       15.68        50.70        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        13.64        56.15        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        0.92         1.22        33.04        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        15.58        26.73        53.88         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
       12.69         3.06         9.67        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB 
        8.58        19.07        22.72         9.01        25.02         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
       14.24         1.84        33.14        51.32        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        12.76        11.90        21.04        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE 
       18.58         3.88         9.63        13.64        21.11         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       88.87        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62        50.04         0.62        51.16        66.54 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.50        17.42         7.33        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       17.88        19.50         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        17.56        36.43        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.79        12.56        13.97        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-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
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-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
      142.78         4.80        13.58        20.81        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        18.81        19.00        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
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-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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
        5.52        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 
       27.45         2.70         7.10        13.35        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       10.65         8.94        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 
       59.31         7.23        20.12        66.02         6.94        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-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
       21.34        19.10        36.49         1.51        19.40        64.01 
TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
       12.16         9.07        11.70        17.72        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
       11.80        44.38         1.15        15.58        21.07        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD 
       76.01        78.25         3.02       112.83        35.24        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG 
        6.21         3.85        45.04         6.58         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       60.16        56.35        19.40         8.52        54.21         5.52 
TCGA-GU-AATO 
       10.65 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.56               0.49 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             94.29             166.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             15.07              17.75 
[1] "0.6 - 94.3 (15.1)"  "0.5 - 166.0 (17.8)"
[1] "hr=" "1.2"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED         1       14        20       20
  17P GAIN WILD-TYPE       1      115       120      115
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  1                  1
  STAGE II                14                115
  STAGE III               20                120
  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  30   7
  17P GAIN WILD-TYPE      108 165  51
D30V4, multiclass
          clus
vv         17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1+T2               15                108
  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
  17P GAIN MUTATED    29   8  13   0
  17P GAIN WILD-TYPE 207  39  62   8
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               29                207
  N1                8                 39
  N2               13                 62
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    26   3
  17P GAIN WILD-TYPE 166   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     26    3
  17P GAIN WILD-TYPE  166    8
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               26                166
  1                3                  8
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    14  42
  17P GAIN WILD-TYPE  93 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     14   42
  17P GAIN WILD-TYPE   93  259
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               14                 93
  MALE                 42                259
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    52   2
  17P GAIN WILD-TYPE 312  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     52    2
  17P GAIN WILD-TYPE  312   18
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                52                312
  YES                2                 18
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, continuous
D30V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       3                         3    48
  17P GAIN WILD-TYPE    40                        19   279
D30V12, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    3                 40
  BLACK OR AFRICAN AMERICAN                3                 19
  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"
D30V13, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     2  48
  17P GAIN WILD-TYPE   7 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2   48
  17P GAIN WILD-TYPE    7  321
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               48                321
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    69  64
  17Q GAIN WILD-TYPE 158 114
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               133                272 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                64                114 
$`17Q GAIN MUTATED`
TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C 
       15.12        12.39        14.89         8.35        20.48        28.70 
TCGA-C4-A0EZ TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 
        8.98        50.27        66.05        17.98        67.36        36.66 
TCGA-DK-AA71 TCGA-DK-AA75 TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ 
       13.64        11.18        25.58        33.04         4.01        24.30 
TCGA-FD-A3SQ TCGA-FD-A5BR TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE 
       46.78        26.73        58.92        62.86        18.81        12.36 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GU-A42P TCGA-GU-AATP 
        4.31        31.07        70.32        21.40        10.92        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND 
       19.82        20.28        27.35         8.58        19.07         9.01 
TCGA-K4-A3WU TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A8HD 
        3.45        46.98        14.24         1.84        86.83        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9T0 TCGA-XF-AAMH TCGA-XF-AAML 
       97.12        15.35         3.22        26.27        11.31         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       71.57        91.73        86.30        13.64        30.28        94.29 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 
        0.62        41.75        10.22        47.80        17.42        40.08 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R 
        2.66         6.74         6.58        12.16        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20X TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A8HY 
       14.96         8.25        12.59        12.13        12.62        11.34 
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-A3WX TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC 
        8.15        10.55        15.02        19.00        15.35        43.59 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-FD-A3B5 
       22.16         0.56        26.96        24.03        13.68         8.94 
TCGA-FD-A3SP TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TF TCGA-FT-A3EE TCGA-G2-AA3F 
       25.74         5.36         7.10         2.27         3.25        29.36 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE 
       18.97        14.27         8.48        19.40        38.60        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41S 
       21.24         9.07        11.70         1.81        11.80         1.15 
TCGA-LC-A66R TCGA-MV-A51V TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       15.32        13.48        37.05        22.68        76.01        69.34 
TCGA-UY-A8OC TCGA-UY-A9PB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SU 
        3.02        29.56         1.87        17.88        48.62         5.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9R9 
      110.60         2.96         8.32        56.48        11.97        28.41 
TCGA-ZF-A9RD TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       13.41        59.38        67.20        35.41         8.52        29.49 
TCGA-GU-AATO 
       10.65 

$`17Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A3PJ 
      108.95        16.27        16.77        33.83        26.14        25.94 
TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        9.96        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       87.32         8.22        17.72        21.30        23.21         9.67 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       64.18        53.29        76.60        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA77 
       52.01       165.73       166.03        13.64        56.15        20.32 
TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
       15.35         0.92         1.22        60.66        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y 
       29.16        19.79        12.85        27.35         3.62        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P 
       53.88        10.78         5.69         8.25        18.08         6.28 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P 
        6.15        12.69         3.06         9.67        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A763 
       33.01        17.62        19.13        17.75        24.92        32.78 
TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       22.72        25.02         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A9SK 
       50.56        35.97        33.14        51.32       125.49        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMJ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 
       54.90        98.99        44.32        30.94        61.45        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
        3.88         9.63        21.11         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-BL-A13I 
       27.62        50.04        51.16        66.54         2.50         7.33 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB 
       13.15        19.04        17.88         5.06        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        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-A9FM TCGA-CU-A3QU TCGA-DK-A1A3 
       12.10        11.34        11.87        13.08         5.19        21.86 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK 
       16.14        17.62        15.62        17.95       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 
       13.58        20.81       163.30        13.58        18.81        12.03 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       38.83        29.72         5.36         2.24        16.70         0.66 
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-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37         8.09        32.02        16.77        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
       27.98         5.52        22.98        14.96        20.91        19.33 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       27.45         2.70        13.35        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.23        20.12        66.02         6.94        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.91        14.07         0.49         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
        2.10         3.12        20.98         2.20        11.31         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
       20.05        15.78         4.73         7.00        21.34        19.10 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
       36.49         1.51        64.01        17.72        15.42        16.27 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       44.38        15.58        21.07        12.23        16.67        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        35.24        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A9SH TCGA-XF-A9SI 
        6.21         3.85        45.04         6.58        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMX 
       66.41        23.64        28.24        16.27        92.98         6.77 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       31.20        35.84        21.86        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 
       20.22         2.89         8.61        60.16        56.35        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5N 
       54.21         5.52 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.56               0.49 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            112.44             166.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             17.42              17.67 
[1] "0.6 - 112.4 (17.4)" "0.5 - 166.0 (17.7)"
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED         1       36        42       55
  17Q GAIN WILD-TYPE       1       93        98       80
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  1                  1
  STAGE II                36                 93
  STAGE III               42                 98
  STAGE IV                55                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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  64  22
  17Q GAIN WILD-TYPE       83 131  36
D31V4, multiclass
          clus
vv         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1+T2               40                 83
  T3                     64                131
  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
  17Q GAIN MUTATED    68  18  34   2
  17Q GAIN WILD-TYPE 168  29  41   6
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               68                168
  N1               18                 29
  N2               34                 41
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    58   4
  17Q GAIN WILD-TYPE 134   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     58    4
  17Q GAIN WILD-TYPE  134    7
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               58                134
  1                4                  7
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    36  99
  17Q GAIN WILD-TYPE  71 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     36   99
  17Q GAIN WILD-TYPE   71  202
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               36                 71
  MALE                 99                202
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   127   4
  17Q GAIN WILD-TYPE 237  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    127    4
  17Q GAIN WILD-TYPE  237   16
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO               127                237
  YES                4                 16
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, continuous
D31V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED      11                         5   112
  17Q GAIN WILD-TYPE    32                        17   215
D31V12, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                   11                 32
  BLACK OR AFRICAN AMERICAN                5                 17
  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"
D31V13, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6 117
  17Q GAIN WILD-TYPE   3 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  117
  17Q GAIN WILD-TYPE    3  252
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  3
  NOT HISPANIC OR LATINO              117                252
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    64  51
  18P GAIN WILD-TYPE 163 127
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               115                290 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                51                127 
$`18P GAIN MUTATED`
TCGA-4Z-AA84 TCGA-BT-A20W TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A3KJ 
       15.12         8.35        28.70         8.98        12.92        18.48 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6W 
       87.32         8.22        66.05        36.66        52.01        13.64 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SR TCGA-FD-A3SS 
       11.18        15.35        33.04        60.66        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C1 
       27.35        15.58        26.73        10.78         8.25        58.92 
TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        6.28        12.36         4.31        31.07        17.23        11.08 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK 
       17.62        70.32        10.92        32.98        19.82        27.35 
TCGA-GV-A40G TCGA-KQ-A41Q TCGA-R3-A69X TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD 
       19.07        46.98        14.24        86.83        51.32        97.45 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9T3 
       15.35         3.22        34.45        14.93         4.21         2.24 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-ZF-AA53 TCGA-4Z-AA7R 
       54.90         7.63        71.57        98.99        57.90        17.16 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-5N-A9KI TCGA-BL-A3JM TCGA-BT-A20V TCGA-BT-A2LB 
        0.62        41.75         2.50         6.74         5.06        16.18 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-E7-A6ME 
       36.43         1.94        12.56         7.79         8.15        24.03 
TCGA-E7-A7PW TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TF 
       13.68         8.94        22.52         5.36        27.45         2.27 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A4ZW 
       61.94        26.93        59.31        29.36        15.91         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
        8.94        26.70         2.10         2.20        11.31         7.63 
TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A5NE 
        7.00        19.10         8.48        36.49        19.40        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R 
       21.24         9.07         1.81        11.80         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A9PB 
       15.58        13.48        17.62        37.05        76.01        29.56 
TCGA-XF-A8HB TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 
       45.04        23.64       110.60         2.96         6.77        56.48 
TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 
       21.86        64.08        20.22        67.20        35.41        54.21 
TCGA-ZF-AA5H 
       29.49 

$`18P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO 
       14.89        20.48        25.94         9.96        18.58         4.90 
TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       15.12        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       46.68        17.72        50.27        21.30        23.21         9.67 
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-AA6R TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA74 
       50.70        38.24       165.73       166.03        13.64        56.15 
TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SJ 
       20.32        25.58         0.92         1.22         4.01        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43X TCGA-FD-A5BS 
       23.41        17.98        29.16        46.78         3.62        53.88 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        5.69        18.08        62.86        18.81         6.15        12.69 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
        3.06         9.67        33.01        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND 
       24.92        32.78        20.28         8.58        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HE TCGA-XF-A8HF 
       50.56        35.97         1.84        33.14       125.49        97.12 
TCGA-XF-A9SK TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       15.98        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR 
       66.64         2.10        13.74        10.82        11.31        91.73 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        9.63        13.64        21.11        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       88.87        34.06        19.69        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       27.62        50.04        51.16        66.54        10.22        47.80 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42        40.08         7.33         2.66         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-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F6 
        8.25        17.16         4.67        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
      142.78         4.80        13.58        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        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-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       24.66        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
       32.02        16.77        12.62        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A62O 
       22.98        14.96        20.91        19.33         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
       13.35        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       48.00        15.95         7.23        20.12        66.02         6.94 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS 
       20.71        15.81        14.07        13.91         3.12        20.98 
TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
       18.97        20.05        15.78         4.73        14.27        21.34 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB 
        1.51        38.60        64.01        11.70        17.72        15.42 
TCGA-K4-A83P TCGA-KQ-A41R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       16.27        44.38        21.07        12.23        16.67        16.54 
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-A8HH 
       35.24        17.82         6.21         3.85         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN4 TCGA-XF-AAN5 
       28.24        16.27        92.98         8.32        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       18.84         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N 
       35.84        28.41        13.41        58.72        47.84         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
        8.61        59.38        60.16        56.35        19.40         8.52 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.49               0.56 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            110.60             166.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            17.230             17.735 
[1] "0.5 - 110.6 (17.2)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1"  
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         0       34        45       37
  18P GAIN WILD-TYPE       2       95        95       98
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                34                 95
  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         30  57  17
  18P GAIN WILD-TYPE       93 138  41
D32V4, multiclass
          clus
vv         18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1+T2               30                 93
  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    66   8  24   3
  18P GAIN WILD-TYPE 170  39  51   5
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               66                170
  N1                8                 39
  N2               24                 51
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    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  83
  18P GAIN WILD-TYPE  74 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     33   83
  18P GAIN WILD-TYPE   74  218
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               33                 74
  MALE                 83                218
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   104   4
  18P GAIN WILD-TYPE 260  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    104    4
  18P GAIN WILD-TYPE  260   16
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO               104                260
  YES                4                 16
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, continuous
D32V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       5                         7   100
  18P GAIN WILD-TYPE    38                        15   227
D32V12, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                7                 15
  WHITE                                  100                227
[1] 3 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     3 105
  18P GAIN WILD-TYPE   6 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3  105
  18P GAIN WILD-TYPE    6  264
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              105                264
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    29  31
  18Q GAIN WILD-TYPE 198 147
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                60                345 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                31                147 
$`18Q GAIN MUTATED`
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-DK-A3IN TCGA-DK-A6B6 TCGA-DK-AA6W TCGA-DK-AA75 
       28.70         8.98         8.22        36.66        13.64        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-FD-A3B6 TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43Y 
       20.32        15.35        33.04        19.79        27.35        15.58 
TCGA-FD-A5BR TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P 
       26.73         6.15        12.36         4.31        31.07        11.08 
TCGA-G2-AA3D TCGA-GU-A42P TCGA-GU-AATP TCGA-R3-A69X TCGA-UY-A78N TCGA-UY-A9PH 
       70.32        10.92        32.98        14.24        86.83        51.32 
TCGA-XF-A8HG TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-AAML TCGA-XF-AAMY TCGA-4Z-AA80 
       15.35        34.45         4.21         7.63        98.99         0.62 
TCGA-4Z-AA81 TCGA-BL-A3JM TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F0 
       41.75         6.74         5.06        16.18        36.43         1.94 
TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-G2-A2EL TCGA-G2-A2EO 
       16.14         7.79         5.36        27.45        26.93        59.31 
TCGA-GC-A6I1 TCGA-GU-A42Q TCGA-GU-AATQ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-K4-A6FZ 
        8.94        11.31         7.00         8.48        36.49         1.81 
TCGA-LT-A5Z6 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A9SG 
       15.58        22.68        76.01        29.56        45.04        48.62 
TCGA-XF-AAN0 TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4X TCGA-ZF-AA58 
       56.48        21.86        64.08        20.22        67.20        54.21 

$`18Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
       18.58        12.92         4.90        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
        2.14        19.00        16.70       130.88        46.68        87.32 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
       17.72        50.27        21.30        23.21         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA71 
       50.70        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA74 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA 
       56.15        25.58         0.92         1.22         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS 
       24.30        23.41        17.98        29.16        46.78        12.85 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
        3.62        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG 
       58.92         6.28        62.86        18.81        12.69         3.06 
TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB 
        9.67        17.23        33.01        17.62        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       17.75        24.92        32.78        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       46.98         1.84        33.14        97.45       125.49        97.12 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
        3.22        15.98        14.93        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ 
       10.82        11.31        54.90        71.57        91.73        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
       13.64        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       34.98        27.62        50.04        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
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-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B 
        5.06        14.96         8.25        17.16         4.67        17.56 
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-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        11.34        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AF 
        1.84        21.86        66.41        18.41       112.44        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62        17.95       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        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-A7PW 
       26.96        26.24         4.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N 
       25.74        22.98        14.96        20.91        19.33         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A3IB 
        8.94         3.25        61.94        48.00        15.95         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         0.49        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        3.12        20.98         2.20        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HO 
       15.78         4.73        14.27        21.34        19.10         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       11.70        17.72        15.42        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        21.07        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OB 
       16.54        38.99        17.62        37.05        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
        3.02       112.83        35.24        17.82         6.21         3.85 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        6.58         1.87        17.88        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
        2.96         8.32         6.77        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U 
       28.41        13.41        58.72        47.84         2.89         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-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.62               0.49 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             98.99             166.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            20.005             17.620 
[1] "0.6 - 99.0 (20.0)"  "0.5 - 166.0 (17.6)"
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         0       23        21       17
  18Q GAIN WILD-TYPE       2      106       119      118
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                23                106
  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
  18Q GAIN MUTATED         20  27   8
  18Q GAIN WILD-TYPE      103 168  50
D33V4, multiclass
          clus
vv         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1+T2               20                103
  T3                     27                168
  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
  18Q GAIN MUTATED    37   4  12   1
  18Q GAIN WILD-TYPE 199  43  63   7
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               37                199
  N1                4                 43
  N2               12                 63
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    16  45
  18Q GAIN WILD-TYPE  91 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     16   45
  18Q GAIN WILD-TYPE   91  256
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               16                 91
  MALE                 45                256
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    57   2
  18Q GAIN WILD-TYPE 307  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     57    2
  18Q GAIN WILD-TYPE  307   18
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                57                307
  YES                2                 18
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, continuous
D33V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       1                         2    54
  18Q GAIN WILD-TYPE    42                        20   273
D33V12, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                 42
  BLACK OR AFRICAN AMERICAN                2                 20
  WHITE                                   54                273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  55
  18Q GAIN WILD-TYPE   7 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   55
  18Q GAIN WILD-TYPE    7  314
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               55                314
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    51  35
  19P GAIN WILD-TYPE 176 143
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                86                319 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                35                143 
$`19P GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-BT-A20N TCGA-CU-A3KJ TCGA-DK-A2HX TCGA-DK-A6AV 
       16.27        15.12        26.14        18.48        46.68        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA75 TCGA-E7-A7DU 
       67.36        15.68       166.03        13.64        11.18         0.92 
TCGA-FD-A3SR TCGA-FD-A43X TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A3VY 
       19.79         3.62         3.06         4.31        31.07        17.62 
TCGA-G2-AA3D TCGA-GC-A3YS TCGA-GV-A40G TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A8HF 
       70.32        24.92        19.07         1.84        51.32        97.12 
TCGA-XF-A8HG TCGA-XF-A9SV TCGA-XF-A9T8 TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-YC-A8S6 
       15.35        12.76        13.74        44.32        18.58         9.63 
TCGA-ZF-A9R2 TCGA-ZF-AA4T TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-5N-A9KM TCGA-BL-A13J 
       21.11        19.69         0.62        51.16        17.42         2.66 
TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CF-A1HS 
        6.74        19.04         8.25        17.16         1.94        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A8HY TCGA-CU-A3YL 
       12.59        12.13        12.46        12.62        11.34        29.79 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2I4 TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 
       21.86        18.41       142.78        19.00        12.03        38.83 
TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-FD-A43U TCGA-FD-A6TF TCGA-FT-A3EE 
        0.56         4.24        24.03        20.91         2.27         3.25 
TCGA-G2-AA3B TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH 
       66.02         4.73         7.00        14.27        21.34         8.48 
TCGA-HQ-A2OE TCGA-K4-A5RH TCGA-K4-AAQO TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A8OB 
       38.60         9.07        11.80        16.54        37.05        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A9SI TCGA-XF-A9SU 
        3.02        35.24        29.56         6.58        79.66         5.98 
TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA51 
       56.48        75.39        64.08        20.22        59.38        56.35 
TCGA-ZF-AA54 TCGA-ZF-AA56 
       19.40         8.52 

$`19P GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W 
      108.95        16.77        33.83        12.39        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL 
       20.48        25.94         9.96        28.70         8.98        18.58 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       12.92         4.90        15.12        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       16.70       130.88        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
       21.30        23.21         9.67        66.05        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       76.60        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV 
       13.64        56.15        20.32        15.35        25.58         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR 
       29.16        46.78        12.85        27.35        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3RB 
        9.67        17.23        11.08        33.01        21.40        19.13 
TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.75        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       27.35         8.58        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE 
       46.98        14.24        33.14        86.83        97.45       125.49 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW 
        3.22        15.98        34.45        14.93         4.21        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YF-AA3M 
       98.99        30.94        61.45        86.30         3.88        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 
       30.28        94.29         3.48        88.87        34.06        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         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-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 
       41.75        66.54        10.22        47.80         2.50        40.08 
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        7.33         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06        14.96         5.06        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MH 
       36.43        28.41        23.01        12.79        13.97        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       12.16        10.95        12.66        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       12.00        12.10        11.34        11.87        13.08         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        1.84        66.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
       17.95         7.79         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       10.55       163.30        15.02        13.58        18.81        15.35 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       43.59        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
        0.66        26.96        26.24        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       22.98        14.96        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        7.10        13.35        10.85        12.66        10.65         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       20.12         6.94        29.36        20.71        15.81        15.91 
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        26.70         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-A764 TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       20.05        15.78        19.10        36.49         1.51        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       64.01        12.16        21.24        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       15.42        16.27        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K 
       21.07        13.48        12.23        16.67        38.99        17.62 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE 
       22.68        76.01        78.25       112.83        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        3.85        45.04         1.87        17.88        48.62        64.80 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
       66.41        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-YC-A89H TCGA-YC-A9TC 
        2.96         8.32         6.77        27.06        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U 
       28.41        13.41        58.72        47.84         2.89         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       60.16        67.20        35.41        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.56               0.49 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            166.03             165.73 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             17.52              17.72 
[1] "0.6 - 166.0 (17.5)" "0.5 - 165.7 (17.7)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         0       28        28       30
  19P GAIN WILD-TYPE       2      101       112      105
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                28                101
  STAGE III               28                112
  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
  19P GAIN MUTATED         26  41  15
  19P GAIN WILD-TYPE       97 154  43
D34V4, multiclass
          clus
vv         19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1+T2               26                 97
  T3                     41                154
  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
  19P GAIN MUTATED    48  10  21   0
  19P GAIN WILD-TYPE 188  37  54   8
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               48                188
  N1               10                 37
  N2               21                 54
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    42   3
  19P GAIN WILD-TYPE 150   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     42    3
  19P GAIN WILD-TYPE  150    8
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               42                150
  1                3                  8
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    18  69
  19P GAIN WILD-TYPE  89 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     18   69
  19P GAIN WILD-TYPE   89  232
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               18                 89
  MALE                 69                232
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    73   5
  19P GAIN WILD-TYPE 291  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     73    5
  19P GAIN WILD-TYPE  291   15
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                73                291
  YES                5                 15
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, continuous
D34V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED      12                         2    69
  19P GAIN WILD-TYPE    31                        20   258
D34V12, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                   12                 31
  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"
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    77  54
  19Q GAIN WILD-TYPE 150 124
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               131                274 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                54                124 
$`19Q GAIN MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A42C TCGA-CU-A3KJ 
       16.27        16.77        15.12        26.14        28.70        18.48 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 
       16.70        46.68        87.32        66.05        64.18        67.36 
TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA75 TCGA-E5-A4TZ 
       15.68        38.24       166.03        13.64        11.18        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X 
       25.58         0.92        24.30        19.79        12.85         3.62 
TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY 
       18.81         3.06         4.31        31.07        17.23        17.62 
TCGA-G2-AA3D TCGA-GC-A3YS TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-HQ-A5ND 
       70.32        24.92        32.98        19.82        20.28         9.01 
TCGA-K4-A3WS TCGA-K4-A4AB TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       25.02         2.76        35.97        46.98        14.24         1.84 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9T3 
       97.12        15.35        15.98        14.93        12.76         2.24 
TCGA-XF-AAMQ TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YC-A8S6 TCGA-YF-AA3M 
       71.57        44.32        86.30        18.58         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-AA4T TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-5N-A9KM 
       21.11        19.69         0.62        41.75        51.16        17.42 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        2.66         6.74        19.04         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A3MF 
       16.18        36.43         1.94        23.01        12.56        12.59 
TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A3YL TCGA-DK-A1A3 
       12.13        12.62        12.00        11.34        29.79        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-AA6P TCGA-DK-AA6U 
       66.41        18.41       142.78        13.58        15.02        19.00 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME 
       12.03        43.59        38.83         0.56         4.24        24.03 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FT-A3EE 
       22.98        20.91        27.45         2.27        10.85         3.25 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OS 
       61.94        59.31        66.02        15.91        14.07        20.98 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH 
       18.97         4.73         7.00        14.27        21.34         8.48 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A5RH TCGA-K4-AAQO TCGA-S5-AA26 TCGA-UY-A78K 
       19.40        38.60         9.07        11.80        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB 
       37.05        69.34         3.02        35.24        29.56        45.04 
TCGA-XF-A8HC TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
        6.58        79.66         5.98         6.77        56.48        75.39 
TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       20.22        59.38        56.35        19.40         8.52 

$`19Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD 
      108.95        33.83        12.39        14.89         8.35        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       25.94         9.96         8.98        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A3IN 
       15.12        13.58         2.14        19.00       130.88         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 
       17.72        50.27        21.30        23.21         9.67        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R 
       53.29        76.60        50.70        36.66        52.01       165.73 
TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       13.64        56.15        20.32         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43P 
       60.66        23.41        17.98        29.16        46.78        27.35 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08        58.92         6.28        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3RB 
       12.36         9.67        11.08        33.01        21.40        19.13 
TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       17.75        10.92        32.78        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
       22.72         3.45         9.14        27.68        52.73        50.56 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SJ 
       33.14        86.83        51.32        97.45       125.49         3.22 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       34.45         4.21        11.90        21.04        26.27        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN8 
        7.63        91.73        98.99        30.94        61.45         3.88 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 
       30.28        94.29         3.48        88.87        34.06        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         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-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        47.80         2.50        40.08         7.33 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.58        13.15        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A27C 
       14.96         4.67        17.56        28.41        12.79        13.97 
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-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        5.19         1.84       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
       17.95         7.79         4.80         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E7-A3X6 TCGA-E7-A3Y1 
      163.30        13.58        18.81        15.35        29.72         5.36 
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-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV 
       27.98         5.52        25.74        14.96        19.33         5.36 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        2.70         7.10        13.35        12.66        10.65         8.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       48.00        15.95        26.93         7.23        20.12         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       29.36        20.71        15.81         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
       26.70         2.10         3.12         2.20        11.31         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF 
       20.05        15.78        19.10        36.49         1.51        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       12.16        21.24        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       16.27        44.38         1.15        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78O 
       13.48        12.23        16.67        38.99        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       78.25       112.83        17.82         6.21         3.85         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ 
       17.88        48.62        64.80        66.41        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 
       16.27        92.98       110.60         2.96         8.32        27.06 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       18.84         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       47.84         2.89         8.61        60.16        67.20        35.41 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.56               0.49 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            166.03             165.73 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             18.48              17.36 
[1] "0.6 - 166.0 (18.5)" "0.5 - 165.7 (17.4)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         0       35        44       52
  19Q GAIN WILD-TYPE       2       94        96       83
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  0                  2
  STAGE II                35                 94
  STAGE III               44                 96
  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
  19Q GAIN MUTATED         34  64  22
  19Q GAIN WILD-TYPE       89 131  36
D35V4, multiclass
          clus
vv         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1+T2               34                 89
  T3                     64                131
  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
  19Q GAIN MUTATED    69  17  32   3
  19Q GAIN WILD-TYPE 167  30  43   5
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               69                167
  N1               17                 30
  N2               32                 43
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    61   5
  19Q GAIN WILD-TYPE 131   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     61    5
  19Q GAIN WILD-TYPE  131    6
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               61                131
  1                5                  6
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    34  98
  19Q GAIN WILD-TYPE  73 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     34   98
  19Q GAIN WILD-TYPE   73  203
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               34                 73
  MALE                 98                203
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   116   4
  19Q GAIN WILD-TYPE 248  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    116    4
  19Q GAIN WILD-TYPE  248   16
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO               116                248
  YES                4                 16
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, continuous
D35V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED      12                         5   107
  19Q GAIN WILD-TYPE    31                        17   220
D35V12, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                   12                 31
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                  107                220
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3 117
  19Q GAIN WILD-TYPE   6 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3  117
  19Q GAIN WILD-TYPE    6  252
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              117                252
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   108  91
  20P GAIN WILD-TYPE 119  87
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               199                206 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                91                 87 
$`20P GAIN MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK 
      108.95        16.27        14.89         8.35        20.48         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       28.70         8.98        12.92         4.90        15.12        18.48 
TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X2 
        2.14       130.88        46.68         8.22        23.21        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA71 
       67.36        15.68        36.66        38.24       165.73        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 
       56.15        11.18        15.35        25.58         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR 
        4.01        60.66        24.30        23.41        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A6TC 
       12.85        27.35         3.62        26.73        10.78         6.15 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FT-A61P TCGA-GC-A3BM TCGA-GC-A3RB 
       12.36         4.31         9.67        11.08        21.40        19.13 
TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-K4-A3WS TCGA-K4-A3WU 
       32.98        20.28         8.58        19.07        25.02         3.45 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD 
       50.56        35.97         1.84        33.14        51.32        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAMQ 
       12.76        21.04         2.24        66.64        10.82        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       91.73        98.99        44.32        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7S 
       94.29        88.87        19.69        24.13        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-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20V 
       40.08         2.66         6.74         6.58         5.06         5.06 
TCGA-BT-A20X TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        8.25        36.43        28.41         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47X 
       12.56        12.59        12.13        12.16        12.66        12.62 
TCGA-CF-A8HX TCGA-CU-A5W6 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       11.34         1.84       112.44        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X 
        4.80        13.58        10.55        15.02        19.00        15.35 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B3 
       43.59        38.83        24.03        13.68         8.09        32.02 
TCGA-FD-A3N5 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S 
       22.52        25.74        22.98        27.45         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
        2.27        10.85        10.65         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       15.95        59.31        29.36        20.71        15.81        15.91 
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        26.70         2.10 
TCGA-GD-A6C6 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        2.20        20.05        15.78        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI 
        8.48        36.49        19.40        12.16         9.07        11.70 
TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41S TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.81        11.80         1.15        13.48        12.23        16.67 
TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC 
       38.99        37.05        22.68        76.01        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SI 
       35.24        29.56         6.21         3.85         1.87        79.66 
TCGA-XF-A9SU TCGA-XF-A9T4 TCGA-XF-AAMT TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        5.98        16.27         2.96        18.84        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       31.20        47.84        20.22         2.89         8.61        59.38 
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        29.49         5.52 
TCGA-GU-AATO 
       10.65 

$`20P GAIN WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A3PJ 
       16.77        15.12        33.83        12.39        26.14        25.94 
TCGA-CF-A9FL TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IQ 
       18.58        13.58        19.00        16.70        87.32        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
       50.27        21.30         9.67        66.05        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA77 
       76.60        50.70        52.01       166.03        13.64        20.32 
TCGA-E7-A7DU TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BX 
        0.92        17.98        29.16        15.58        53.88         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY 
       12.69         3.06        31.07        17.23        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ 
       70.32        17.75        24.92        10.92        32.78        19.82 
TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       27.35        22.72         9.01         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X TCGA-UY-A78N TCGA-XF-A8HE TCGA-XF-A9ST 
       52.73        46.98        14.24        86.83       125.49         4.21 
TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH 
       11.90        26.27        18.90         2.10        13.74        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       54.90         7.63        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.88         9.63         3.48        34.06        57.90        12.23 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7R 
       11.97        94.88       104.65         8.35        16.83        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0YX 
       27.62        50.04        51.16        17.42         7.33        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LA 
       19.04        12.16        17.88        19.50        14.96        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47S 
       16.18         4.67        17.56        13.97        13.08        10.95 
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-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
       11.34        11.87        13.08         5.19        29.79        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IM 
       66.41        18.41        16.14        17.62        15.62         8.15 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 TCGA-E7-A3X6 
       20.81       163.30        13.58        18.81        12.03        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H 
       26.96        26.24         4.24        24.66        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
       15.32        14.37        16.77         8.94        12.62        27.98 
TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N 
        5.52        14.96        20.91        19.33         5.36         2.70 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       12.66         8.94        26.93         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        6.94         3.12        20.98        11.31        18.97         7.63 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV 
        4.73         7.00         1.51        38.60        64.01        21.24 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 
       17.72        15.42        16.27        44.38        15.32        15.58 
TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
       21.07        16.54        17.62        78.25       112.83        17.82 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL 
       45.04         6.58        17.88        48.62        64.80        66.41 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX 
       23.64        28.24        92.98       110.60         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 
       56.48        27.06        75.39         0.66        11.97        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4W 
       21.86        28.41        13.41        64.08        58.72        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA56 
       67.20         8.52 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.49               0.56 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            165.73             166.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             16.67              17.67 
[1] "0.5 - 165.7 (16.7)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.1"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         1       59        66       75
  20P GAIN WILD-TYPE       1       70        74       60
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  1                  1
  STAGE II                59                 70
  STAGE III               66                 74
  STAGE IV                75                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2 T3 T4
  20P GAIN MUTATED         55 98 32
  20P GAIN WILD-TYPE       68 97 26
D36V4, multiclass
          clus
vv         20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1+T2               55                 68
  T3                     98                 97
  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   105  26  40   7
  20P GAIN WILD-TYPE 131  21  35   1
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              105                131
  N1               26                 21
  N2               40                 35
  N3                7                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    88   8
  20P GAIN WILD-TYPE 104   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     88    8
  20P GAIN WILD-TYPE  104    3
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               88                104
  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  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    181    6
  20P GAIN WILD-TYPE  183   14
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               181                183
  YES                6                 14
[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   123 105
  20Q GAIN WILD-TYPE 104  73
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               228                177 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               105                 73 
$`20Q GAIN MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD 
      108.95        16.27        26.14        14.89         8.35        20.48 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        9.96        28.70         8.98        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IS 
       18.48         2.14       130.88        46.68         8.22        50.27 
TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       23.21        17.98        64.18        67.36        15.68        36.66 
TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       38.24       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       11.18        15.35        25.58         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       60.66        24.30        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TC 
        3.62        26.73        10.78        18.08        58.92         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FT-A61P 
       12.69        12.36         4.31         9.67        31.07        11.08 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-AATP 
       17.62        70.32        21.40        19.13        24.92        32.98 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-KQ-A41O 
       20.28         8.58        25.02         3.45         9.14        50.56 
TCGA-KQ-A41P TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF 
       35.97         1.84        33.14        51.32        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV 
       15.35         3.22        15.98        34.45        14.93        12.76 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMQ 
       21.04         2.24        66.64         2.10        10.82        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-YF-AA3M TCGA-ZF-A9R2 
       91.73        98.99        44.32        30.94        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-2F-A9KP 
       30.28        94.29        88.87        19.69        24.13        11.97 
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 
      104.65        44.94        34.98         0.62        41.75        66.54 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       47.80         2.50        17.42        40.08         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20Q TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42E 
        6.58        19.04        19.50         5.06         8.25        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF 
       28.41         1.94        23.01        12.79        12.56        12.59 
TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47X TCGA-CF-A8HX 
       12.13        12.16        10.95        12.66        12.62        11.34 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 
        1.84        66.41        18.41       112.44        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6U 
      142.78        13.58         8.15        10.55        15.02        19.00 
TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7PW 
       15.35        43.59        38.83        22.16        24.03        13.68 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3N5 TCGA-FD-A3SP TCGA-FD-A43N 
       12.95         8.09        32.02        22.52        25.74        22.98 
TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3ZE 
       27.45         7.10        13.35         2.27        10.85        10.65 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-AA3B 
        3.25        61.94        48.00        15.95        59.31        66.02 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW 
       29.36        20.71        15.81        15.91        14.07         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42Q TCGA-GU-A42R 
        8.94        13.91        26.70         2.10        11.31        18.97 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
       15.78        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ 
       19.40        38.60        64.01         9.07        11.70         1.81 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       11.80         1.15        15.58        13.48        12.23        16.67 
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-XF-A8HB 
        3.02        35.24        29.56         6.21         3.85        45.04 
TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAMT 
        1.87        79.66         5.98        23.64        16.27         2.96 
TCGA-XF-AAMX TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
        6.77        22.36        25.41        31.20        21.86        13.41 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA51 
       58.72        47.84        20.22         2.89         8.61        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       35.41        19.40        54.21        29.49         5.52        10.65 

$`20Q GAIN WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A3PJ TCGA-CF-A9FL 
       16.77        15.12        33.83        12.39        25.94        18.58 
TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IT 
       13.58        19.00        16.70        87.32        17.72        21.30 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6M 
        9.67        66.05        53.29        76.60        50.70        52.01 
TCGA-DK-AA77 TCGA-E7-A7DU TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A43Y 
       20.32         0.92        23.41        17.98        29.16        15.58 
TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
       53.88         5.69         8.25         6.28        62.86        18.81 
TCGA-FD-A6TG TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 
        3.06        17.23        33.01        17.75        10.92        32.78 
TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A4AB 
       19.82        27.35        19.07        22.72         9.01         2.76 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X TCGA-UY-A78N TCGA-XF-A8HE 
       27.68        52.73        46.98        14.24        86.83       125.49 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T8 TCGA-XF-AAMH 
        4.21        11.90        26.27        18.90        13.74        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       54.90         7.63        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KQ 
        9.63         3.48        34.06        57.90        12.23        94.88 
TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 
        8.35        16.83        17.16        27.62        50.04        51.16 
TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R 
       10.22         7.33        13.15        12.16        17.88         5.06 
TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-CF-A27C 
       14.96        17.16        16.18         4.67        17.56        13.97 
TCGA-CF-A3MH TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       13.08        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.10        11.34        11.87        13.08         5.19        29.79 
TCGA-DK-A1A3 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3WW 
       21.86        16.14        17.62        15.62         4.80        20.81 
TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 TCGA-E7-A3X6 TCGA-E7-A3Y1 
      163.30        13.58        18.81        12.03        29.72         5.36 
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-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 
        4.24        24.66        14.07        15.32        14.37        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U 
        8.94        12.62        27.98         5.52        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EL 
       19.33         5.36         2.70        12.66         8.94        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        7.23        20.12         6.94         3.12        20.98         2.20 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATQ TCGA-H4-A2HO TCGA-HQ-A5NE 
        7.63        20.05         4.73         7.00         1.51        12.16 
TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R TCGA-LC-A66R 
       21.24        17.72        15.42        16.27        44.38        15.32 
TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HC 
       21.07        16.54        78.25       112.83        17.82         6.58 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SZ TCGA-XF-AAME 
       17.88        48.62        64.80        66.41        28.24        92.98 
TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
      110.60         8.32        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-AA4V 
        0.66        11.97        35.84        28.41        64.08        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA56 
       60.16        67.20         8.52 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.49               0.56 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            166.03             163.30 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            18.445             17.160 
[1] "0.5 - 166.0 (18.4)" "0.6 - 163.3 (17.2)"
[1] "hr=" "1"  
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         1       68        77       83
  20Q GAIN WILD-TYPE       1       61        63       52
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  1                  1
  STAGE II                68                 61
  STAGE III               77                 63
  STAGE IV                83                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  20Q GAIN MUTATED         64 112  35
  20Q GAIN WILD-TYPE       59  83  23
D37V4, multiclass
          clus
vv         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1+T2               64                 59
  T3                    112                 83
  T4                     35                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q GAIN MUTATED   122  26  49   7
  20Q GAIN WILD-TYPE 114  21  26   1
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              122                114
  N1               26                 21
  N2               49                 26
  N3                7                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   101   7
  20Q GAIN WILD-TYPE  91   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    101    7
  20Q GAIN WILD-TYPE   91    4
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              101                 91
  1                7                  4
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    66 164
  20Q GAIN WILD-TYPE  41 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     66  164
  20Q GAIN WILD-TYPE   41  137
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               66                 41
  MALE                164                137
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   204  10
  20Q GAIN WILD-TYPE 160  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    204   10
  20Q GAIN WILD-TYPE  160   10
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               204                160
  YES               10                 10
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, continuous
D37V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED      17                        10   191
  20Q GAIN WILD-TYPE    26                        12   136
D37V12, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                   17                 26
  BLACK OR AFRICAN AMERICAN               10                 12
  WHITE                                  191                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3 208
  20Q GAIN WILD-TYPE   6 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  208
  20Q GAIN WILD-TYPE    6  161
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              208                161
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    69  47
  21Q GAIN WILD-TYPE 158 131
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               116                289 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                47                131 
$`21Q GAIN MUTATED`
TCGA-4Z-AA7M TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK 
       16.27        12.39        26.14         8.35        20.48         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A3KJ TCGA-DK-A2I6 TCGA-DK-A3IS 
       28.70         8.98        18.58        18.48        87.32        50.27 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6S 
        9.67        66.05        17.98        67.36        15.68       166.03 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       11.18        15.35        33.04         4.01        60.66        24.30 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE 
       29.16        19.79        18.08         6.28         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GU-A42P 
        3.06         4.31        17.23        17.62        21.40        10.92 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-K4-A3WU TCGA-KQ-A41P TCGA-KQ-A41Q 
       20.28         8.58        19.07         3.45        35.97        46.98 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SM 
       86.83        51.32        97.45        97.12         3.22        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-YF-AA3M 
       14.93         4.21        91.73        98.99        44.32        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KQ 
       30.28        94.29        88.87        19.69        12.23        94.88 
TCGA-4Z-AA81 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CF-A1HS 
       41.75        40.08         2.66        17.16         1.94        12.56 
TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A47V TCGA-CF-A8HY TCGA-DK-A1A3 TCGA-DK-A1A7 
       13.97        12.13        12.46        11.34        21.86        18.41 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6P 
       17.95       142.78         4.80        13.58         8.15        15.02 
TCGA-DK-AA6U TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3SP 
       19.00        22.16        24.03        13.68         8.09        25.74 
TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A62O TCGA-G2-A2EK TCGA-G2-AA3B TCGA-GC-A4ZW 
       22.98        27.45         7.10        15.95        66.02         0.49 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HQ 
       13.91        26.70         2.10        21.34        19.10        19.40 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-SY-A9G5 
        1.81        15.42         1.15        15.32        13.48        38.99 
TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SU 
       22.68         3.02         6.21         3.85         1.87         5.98 
TCGA-XF-A9SZ TCGA-XF-AAMX TCGA-ZF-A9R1 TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA4V 
       28.24         6.77        25.41        47.84         8.61        59.38 
TCGA-ZF-AA51 TCGA-ZF-AA52 
       56.35        35.41 

$`21Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20T TCGA-BT-A3PJ 
      108.95        16.77        15.12        33.83        14.89        25.94 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       12.92         4.90        15.12        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
       16.70       130.88        46.68         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 
       23.21        64.18        53.29        76.60        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       38.24        52.01       165.73        13.64        13.64        56.15 
TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SL TCGA-FD-A3SM 
       20.32        25.58         0.92         1.22        23.41        17.98 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       46.78        12.85        27.35         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TA 
       53.88        10.78         5.69         8.25        58.92        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES 
       18.81        12.69         9.67        31.07        11.08        33.01 
TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP 
       70.32        19.13        17.75        24.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB 
       19.82        27.35        22.72         9.01        25.02         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-R3-A69X TCGA-S5-A6DX 
        9.14        27.68        52.73        50.56        14.24         1.84 
TCGA-SY-A9G0 TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SV TCGA-XF-A9SW 
       33.14       125.49        15.35        15.98        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KP 
       21.11         3.48        34.06        57.90        24.13        11.97 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       27.62        50.04         0.62        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 
       47.80         2.50        17.42         7.33         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       14.96         5.06         8.25        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MH 
       36.43        28.41        23.01        12.79        12.59        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       12.16        10.95        12.66        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE 
        5.19        29.79         1.84        66.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       17.62        15.62         7.79        20.81        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       13.58        18.81        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       29.72         5.36         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H 
       26.96        26.24         4.24        24.66        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       15.32        14.37        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
       22.52        27.98         5.52        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        5.36         2.70        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
       10.65         8.94         3.25        61.94        48.00        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
       59.31         7.23        20.12         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.81        15.91        14.07         8.94         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
        4.73         7.00        14.27         8.48        36.49         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       17.72        16.27        11.80        44.38        15.58        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O 
       12.23        16.67        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        35.24        29.56        17.82 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       45.04         6.58        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
       66.41        23.64        16.27        92.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        8.32        56.48        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       11.97        22.36        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4W 
       13.41        64.08        58.72        20.22         2.89        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       67.20        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.49               0.56 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            166.03             165.73 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             18.03              17.56 
[1] "0.5 - 166.0 (18.0)" "0.6 - 165.7 (17.6)"
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         1       32        41       42
  21Q GAIN WILD-TYPE       1       97        99       93
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  1                  1
  STAGE II                32                 97
  STAGE III               41                 99
  STAGE IV                42                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  21Q GAIN MUTATED         31  61  14
  21Q GAIN WILD-TYPE       92 134  44
D38V4, multiclass
          clus
vv         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1+T2               31                 92
  T3                     61                134
  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
  21Q GAIN MUTATED    59  12  27   2
  21Q GAIN WILD-TYPE 177  35  48   6
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               59                177
  N1               12                 35
  N2               27                 48
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    53   3
  21Q GAIN WILD-TYPE 139   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     53    3
  21Q GAIN WILD-TYPE  139    8
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               53                139
  1                3                  8
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    25  91
  21Q GAIN WILD-TYPE  82 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     25   91
  21Q GAIN WILD-TYPE   82  210
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               25                 82
  MALE                 91                210
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED   102   4
  21Q GAIN WILD-TYPE 262  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    102    4
  21Q GAIN WILD-TYPE  262   16
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO               102                262
  YES                4                 16
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, continuous
D38V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED      11                         4    97
  21Q GAIN WILD-TYPE    32                        18   230
D38V12, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                   11                 32
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   97                230
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2 108
  21Q GAIN WILD-TYPE   7 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2  108
  21Q GAIN WILD-TYPE    7  261
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO              108                261
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    21  27
  22Q GAIN WILD-TYPE 206 151
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                48                357 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                27                151 
$`22Q GAIN MUTATED`
TCGA-BT-A20W TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-AA77 TCGA-E7-A541 
        8.35        87.32        50.27        23.21        20.32        25.58 
TCGA-FD-A3B7 TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GV-A3JZ TCGA-GV-A3QK 
        4.01        33.01        70.32        21.40        19.82        27.35 
TCGA-GV-A40E TCGA-KQ-A41P TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-AAML TCGA-XF-AAMQ 
        8.58        35.97         1.84        33.14         7.63        71.57 
TCGA-XF-AAMR TCGA-ZF-A9R4 TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-5N-A9KM 
       91.73        30.28       104.65        44.94        34.98        17.42 
TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A2LB TCGA-CF-A8HY TCGA-DK-A1A6 TCGA-DK-A1AD 
       40.08         6.58        16.18        11.34        66.41       112.44 
TCGA-DK-A3WX TCGA-E7-A4IJ TCGA-FD-A62O TCGA-G2-A2EO TCGA-GC-A3I6 TCGA-GC-A3RD 
       10.55        22.16         7.10        59.31        20.71        14.07 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-KQ-A41R 
        4.73        14.27         8.48        36.49        38.60        44.38 
TCGA-LT-A5Z6 TCGA-UY-A78O TCGA-XF-A9SI TCGA-XF-AAMW TCGA-XF-AAMX TCGA-ZF-A9R0 
       15.58        76.01        79.66         8.32         6.77        22.36 

$`22Q GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       26.14        14.89        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
        8.22        17.72        21.30         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       36.66        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV 
       13.64        56.15        11.18        15.35         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       33.04        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y 
       46.78        19.79        12.85        27.35         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       11.08        17.62        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       32.78        32.98        20.28        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD 
       50.56        46.98        14.24        86.83        51.32        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
      125.49        97.12        15.35         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       11.31        54.90        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7O 
       12.23        24.13        11.97        94.88         8.35        16.83 
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-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A13I TCGA-BL-A13J 
       66.54        10.22        47.80         2.50         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH 
        5.06        14.96         5.06         8.25        17.16         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        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-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AE 
        5.19        29.79         1.84        21.86        18.41        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
       13.58         8.15        20.81       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       29.72         5.36         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-A7PW 
       26.96        26.24         4.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
       27.45         2.70        13.35         2.27        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-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       26.93         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91         0.49         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
        7.63        20.05        15.78         7.00        21.34        19.10 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
        1.51        19.40        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        21.07        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P 
       16.54        38.99        17.62        37.05        22.68        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        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI 
        6.21         3.85        45.04         6.58         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       48.62        64.80        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN4 
       16.27        92.98       110.60         2.96        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39        18.84         0.66        11.97        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.84               0.49 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            112.44             166.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            22.785             17.160 
[1] "1.8 - 112.4 (22.8)" "0.5 - 166.0 (17.2)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED         1       18        15       13
  22Q GAIN WILD-TYPE       1      111       125      122
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  1                  1
  STAGE II                18                111
  STAGE III               15                125
  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         19  19   7
  22Q GAIN WILD-TYPE      104 176  51
D39V4, multiclass
          clus
vv         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1+T2               19                104
  T3                     19                176
  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    28   4   7   2
  22Q GAIN WILD-TYPE 208  43  68   6
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               28                208
  N1                4                 43
  N2                7                 68
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    25   1
  22Q GAIN WILD-TYPE 167  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     25    1
  22Q GAIN WILD-TYPE  167   10
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               25                167
  1                1                 10
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    12  36
  22Q GAIN WILD-TYPE  95 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     12   36
  22Q GAIN WILD-TYPE   95  265
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               12                 95
  MALE                 36                265
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    46   2
  22Q GAIN WILD-TYPE 318  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     46    2
  22Q GAIN WILD-TYPE  318   18
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                46                318
  YES                2                 18
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, continuous
D39V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       3                         3    40
  22Q GAIN WILD-TYPE    40                        19   287
D39V12, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    3                 40
  BLACK OR AFRICAN AMERICAN                3                 19
  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"
D39V13, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  42
  22Q GAIN WILD-TYPE   9 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   42
  22Q GAIN WILD-TYPE    9  327
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               42                327
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    37  28
  XP GAIN WILD-TYPE 190 150
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               65               340 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               28               150 
$`XP GAIN MUTATED`
TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A42C TCGA-DK-A1AC TCGA-FD-A43P TCGA-FD-A6TI 
       16.27        26.14        28.70       130.88        27.35         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-K4-A54R 
       31.07        17.23        10.92        32.98        19.82        27.68 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ 
       66.64        13.74        11.31        71.57        98.99        44.32 
TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA87 TCGA-BL-A13J 
       18.58        21.11         0.62        41.75        47.80         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A2LB TCGA-CF-A1HS 
        6.74         6.58        17.88        19.50        16.18        12.56 
TCGA-CF-A5UA TCGA-CF-A8HX TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-E7-A4IJ TCGA-E7-A7PW 
       12.00        11.34        66.41        16.14        22.16        13.68 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A62S TCGA-FT-A3EE TCGA-G2-AA3B TCGA-GC-A3I6 
       12.95         8.09        13.35         3.25        66.02        20.71 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A767 
        8.94        13.91        26.70        20.98         2.20         4.73 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A78O 
        8.48        36.49        38.60        13.48        17.62        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HI 
       69.34         3.02        17.82         3.85         6.58        17.88 
TCGA-XF-AAMG TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9RF TCGA-ZF-AA4V 
      110.60         6.77        11.97        64.08        59.38 

$`XP GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T 
      108.95        16.77        15.12        33.83        12.39        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL 
        8.35        20.48        25.94         9.96         8.98        18.58 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       12.92         4.90        15.12        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       19.00        16.70        46.68        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       36.66        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        56.15        11.18        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        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-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
        3.62        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FT-A61P 
        6.15        12.69        12.36         3.06         4.31        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       24.92        32.78        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       52.73        50.56        35.97        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       33.14        86.83        51.32        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       15.35         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAN1 
        2.10        10.82        54.90         7.63        91.73        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 
       61.45        86.30         3.88         9.63        13.64        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         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-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       51.16        66.54        10.22         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U 
        7.33        13.15        19.04        12.16         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        5.06         8.25        17.16         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF 
       28.41         1.94        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-A8HY 
       12.10        12.62        12.26        13.12        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
       18.41       112.44        17.62        15.62        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
      142.78         4.80        13.58         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       12.03        43.59        38.83        29.72         5.36         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-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
       24.03        24.66        14.07        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
       27.45         2.70         7.10         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       10.65         8.94        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
       59.31         7.23        20.12         6.94        29.36        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42Q 
       15.91        14.07         0.49         2.10         3.12        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV 
       18.97         7.63        20.05        15.78         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE 
       21.34        19.10         1.51        19.40        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L 
       21.07        12.23        16.67        16.54        38.99        37.05 
TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE 
       22.68        78.25       112.83        35.24        29.56         6.21 
TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
       45.04         1.87        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT 
        5.98        23.64        28.24        16.27        92.98         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        8.32        56.48        27.06        75.39        18.84         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       13.41        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.62              0.49 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           130.88            166.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            17.82             17.62 
[1] "0.6 - 130.9 (17.8)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP GAIN MUTATED         0       17        25       22
  XP GAIN WILD-TYPE       2      112       115      113
D40V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               17               112
  STAGE III              25               115
  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
  XP GAIN MUTATED         18  32  10
  XP GAIN WILD-TYPE      105 163  48
D40V4, multiclass
          clus
vv         XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1+T2              18               105
  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 GAIN MUTATED    37   9  12   2
  XP GAIN WILD-TYPE 199  38  63   6
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              37               199
  N1               9                38
  N2              12                63
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    27   0
  XP GAIN WILD-TYPE 165  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     27    0
  XP GAIN WILD-TYPE  165   11
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              27               165
  1               0                11
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    19  46
  XP GAIN WILD-TYPE  88 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     19   46
  XP GAIN WILD-TYPE   88  255
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              19                88
  MALE                46               255
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    61   0
  XP GAIN WILD-TYPE 303  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     61    0
  XP GAIN WILD-TYPE  303   20
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               61               303
  YES               0                20
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, continuous
D40V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       7                         5    50
  XP GAIN WILD-TYPE    36                        17   277
D40V12, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   7                36
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                  50               277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    25  20
  XQ GAIN WILD-TYPE 202 158
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               45               360 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               20               158 
$`XQ GAIN MUTATED`
TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A42C TCGA-CU-A0YN TCGA-DK-AA6L TCGA-FD-A3B6 
       16.27        26.14        28.70        12.92        38.24        33.04 
TCGA-FD-A43P TCGA-FD-A6TC TCGA-FD-A6TI TCGA-GU-AATP TCGA-GV-A3JZ TCGA-XF-A9SM 
       27.35         6.15         9.67        32.98        19.82        34.45 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY 
       66.64        13.74        11.31         7.63        71.57        98.99 
TCGA-XF-AAMZ TCGA-ZF-A9R2 TCGA-4Z-AA81 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BL-A3JM 
       44.32        21.11        41.75        47.80         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A20P TCGA-BT-A20Q TCGA-CF-A1HS TCGA-CF-A5UA TCGA-CF-A8HX 
        6.58        17.88        19.50        12.56        12.00        11.34 
TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-E7-A7PW TCGA-E7-A85H TCGA-GC-A3I6 TCGA-GC-A6I1 
       66.41        16.14        13.68        12.95        20.71         8.94 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GV-A3QH TCGA-MV-A51V TCGA-UY-A78O TCGA-UY-A8OB 
       26.70        20.98         8.48        13.48        76.01        69.34 
TCGA-UY-A8OC TCGA-XF-AAMX TCGA-ZF-AA4V 
        3.02         6.77        59.38 

$`XQ GAIN WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T 
      108.95        16.77        15.12        33.83        12.39        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL 
        8.35        20.48        25.94         9.96         8.98        18.58 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
        4.90        15.12        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       16.70       130.88        46.68        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        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-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       36.66        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       56.15        11.18        20.32        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        1.22         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y 
       29.16        46.78        19.79        12.85         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
       58.92         6.28        62.86        18.81        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        3.06         4.31        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       10.92        32.78        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
        1.84        33.14        86.83        51.32        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST 
       97.12        15.35         3.22        15.98        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 
        2.10        10.82        54.90        91.73        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 
       86.30        18.58         3.88         9.63        13.64        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         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-AA86 TCGA-5N-A9KI TCGA-5N-A9KM 
        0.62        51.16        66.54        10.22         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R 
       40.08         7.33        13.15        19.04        12.16         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        36.43        28.41         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-A7I0 TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.10        11.34        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG 
        1.84        21.86        18.41       112.44        17.62        15.62 
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-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        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-A7XN 
       26.96        26.24         4.24        24.03        24.66        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       15.32        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP 
       15.81        15.91        14.07         0.49        13.91         2.10 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        3.12         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       21.07        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        22.68        78.25       112.83        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       17.82         6.21         3.85        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
       23.64        28.24        16.27        92.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        8.32        56.48        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89         8.61        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             2.66              0.49 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            98.99            166.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            19.50             17.62 
[1] "2.7 - 99.0 (19.5)"  "0.5 - 166.0 (17.6)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         0       13        19       13
  XQ GAIN WILD-TYPE       2      116       121      122
D41V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 0                 2
  STAGE II               13               116
  STAGE III              19               121
  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
  XQ GAIN MUTATED         12  23   7
  XQ GAIN WILD-TYPE      111 172  51
D41V4, multiclass
          clus
vv         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1+T2              12               111
  T3                    23               172
  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
  XQ GAIN MUTATED    29   7   5   1
  XQ GAIN WILD-TYPE 207  40  70   7
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              29               207
  N1               7                40
  N2               5                70
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    20   0
  XQ GAIN WILD-TYPE 172  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     20    0
  XQ GAIN WILD-TYPE  172   11
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              20               172
  1               0                11
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    12  33
  XQ GAIN WILD-TYPE  95 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     12   33
  XQ GAIN WILD-TYPE   95  268
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              12                95
  MALE                33               268
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    43   0
  XQ GAIN WILD-TYPE 321  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     43    0
  XQ GAIN WILD-TYPE  321   20
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               43               321
  YES               0                20
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, continuous
D41V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       5                         3    36
  XQ GAIN WILD-TYPE    38                        19   291
D41V12, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   5                38
  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  39
  XQ GAIN WILD-TYPE   8 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   39
  XQ GAIN WILD-TYPE    8  330
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              39               330
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    15  16
  1P LOSS WILD-TYPE 212 162
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               31               374 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16               162 
$`1P LOSS MUTATED`
TCGA-BT-A3PK TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A6B6 
        9.96         4.90        15.12        17.72        21.30        36.66 
TCGA-FD-A62P TCGA-FD-A6TE TCGA-GU-AATP TCGA-K4-A3WS TCGA-KQ-A41P TCGA-S5-A6DX 
        6.28        12.36        32.98        25.02        35.97         1.84 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-AAN2 TCGA-ZF-A9RL 
       97.12        15.35         3.22        15.98        61.45        88.87 
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-CF-A47X TCGA-DK-AA6Q TCGA-DK-AA76 TCGA-E5-A2PC 
       24.13         0.62        12.62        13.58        12.03        43.59 
TCGA-FJ-A3ZE TCGA-GU-A766 TCGA-GV-A3QI TCGA-PQ-A6FI TCGA-UY-A78O TCGA-UY-A8OD 
       10.65        15.78        36.49        12.23        76.01       112.83 
TCGA-ZF-A9R3 
       31.20 

$`1P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
       26.14        14.89         8.35        20.48        25.94        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
        8.98        18.58        12.92        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       19.00        16.70       130.88        46.68        87.32         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       50.27        23.21         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08        58.92        62.86        18.81         6.15        12.69 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       24.92        10.92        32.78        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB 
        8.58        19.07        22.72         9.01         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X 
        9.14        27.68        52.73        50.56        46.98        14.24 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SM 
       33.14        86.83        51.32        97.45       125.49        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       11.31        54.90         7.63        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       44.32        30.94        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R 
       13.64        21.11        30.28        94.29         3.48        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       19.69        57.90        12.23        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       50.04        41.75        51.16        66.54        10.22        47.80 
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-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-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        17.56        36.43        28.41         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-A47Y 
       12.16        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
        7.79       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       10.55       163.30        15.02        18.81        19.00        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
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-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-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
        2.27        10.85        12.66         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
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        26.70         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-A764 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       20.05         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
        8.48         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       21.07        13.48        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       37.05        22.68        78.25        69.34         3.02        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         6.21         3.85        45.04         6.58 
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-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R5 
       18.84         0.66        11.97        22.36        25.41        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        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        67.20 
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        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.62              0.49 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           112.83            166.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            15.98             17.67 
[1] "0.6 - 112.8 (16.0)" "0.5 - 166.0 (17.7)"
[1] "hr=" "1.1"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         0       13         6       12
  1P LOSS WILD-TYPE       2      116       134      123
D42V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               13               116
  STAGE III               6               134
  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
  1P LOSS MUTATED         13  13   1
  1P LOSS WILD-TYPE      110 182  57
D42V4, multiclass
          clus
vv         1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1+T2              13               110
  T3                    13               182
  T4                     1                57
[1] 3 2
[1] TRUE
[1] "dimension of 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   6   2
  1P LOSS WILD-TYPE 220  43  69   6
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              16               220
  N1               4                43
  N2               6                69
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    10   2
  1P LOSS WILD-TYPE 182   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     10    2
  1P LOSS WILD-TYPE  182    9
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              10               182
  1               2                 9
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6  25
  1P LOSS WILD-TYPE 101 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6   25
  1P LOSS WILD-TYPE  101  276
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               6               101
  MALE                25               276
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    29   2
  1P LOSS WILD-TYPE 335  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     29    2
  1P LOSS WILD-TYPE  335   18
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               29               335
  YES               2                18
[1] 2 2
[1] FALSE
D42V9, continuous
D42V10, continuous
D42V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         1    29
  1P LOSS WILD-TYPE    42                        21   298
D42V12, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                42
  BLACK OR AFRICAN AMERICAN               1                21
  WHITE                                  29               298
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  30
  1P LOSS WILD-TYPE   9 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   30
  1P LOSS WILD-TYPE    9  339
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              30               339
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    14  17
  1Q LOSS WILD-TYPE 213 161
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               31               374 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               17               161 
$`1Q LOSS MUTATED`
TCGA-BT-A3PK TCGA-CU-A0YO TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X1 
        9.96         4.90        46.68        17.72        21.30        66.05 
TCGA-DK-A6B6 TCGA-FD-A62P TCGA-FD-A6TE TCGA-GU-AATP TCGA-KQ-A41P TCGA-S5-A6DX 
       36.66         6.28        12.36        32.98        35.97         1.84 
TCGA-XF-A8HF TCGA-XF-AAN2 TCGA-ZF-A9RL TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-DK-AA6Q 
       97.12        61.45        88.87        24.13         0.62        13.58 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-FD-A62S TCGA-G2-A3IE TCGA-GC-A3RC 
       12.03        43.59        22.16        13.35        20.12        15.91 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3QH TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A8HC 
       20.05        15.78         8.48        76.01       112.83         6.58 
TCGA-ZF-A9R3 
       31.20 

$`1Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
       26.14        14.89         8.35        20.48        25.94        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
        8.98        18.58        12.92        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN 
        2.14        19.00        16.70       130.88        87.32         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       50.27        23.21         9.67        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M 
       76.60        67.36        15.68        50.70        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y 
       46.78        19.79        12.85        27.35         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG 
       58.92        62.86        18.81         6.15        12.69         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       10.92        32.78        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       19.07        22.72         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X 
        9.14        27.68        52.73        50.56        46.98        14.24 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       33.14        86.83        51.32        97.45       125.49        15.35 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 
       71.57        91.73        98.99        44.32        30.94        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
       94.29         3.48        34.06        19.69        57.90        12.23 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         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-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        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-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.34        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       29.79         1.84        21.86        66.41        18.41       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-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 
       15.02        18.81        19.00        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        5.36         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.70         7.10         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
       59.31         7.23        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        14.07         0.49         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        7.63         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       21.07        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       17.62        37.05        22.68        78.25        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       35.24        29.56        17.82         6.21         3.85        45.04 
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-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R5 
       18.84         0.66        11.97        22.36        25.41        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        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        67.20 
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        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.62              0.49 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           112.83            166.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            20.12             17.59 
[1] "0.6 - 112.8 (20.1)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.1"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED         0       16         5       10
  1Q LOSS WILD-TYPE       2      113       135      125
D43V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               16               113
  STAGE III               5               135
  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
  1Q LOSS MUTATED         13  12   1
  1Q LOSS WILD-TYPE      110 183  57
D43V4, multiclass
          clus
vv         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1+T2              13               110
  T3                    12               183
  T4                     1                57
[1] 3 2
[1] TRUE
[1] "dimension of 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   6   1
  1Q LOSS WILD-TYPE 221  44  69   7
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              15               221
  N1               3                44
  N2               6                69
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    12   1
  1Q LOSS WILD-TYPE 180  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     12    1
  1Q LOSS WILD-TYPE  180   10
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              12               180
  1               1                10
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9  22
  1Q LOSS WILD-TYPE  98 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   22
  1Q LOSS WILD-TYPE   98  279
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               9                98
  MALE                22               279
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    30   0
  1Q LOSS WILD-TYPE 334  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     30    0
  1Q LOSS WILD-TYPE  334   20
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               30               334
  YES               0                20
[1] 2 2
[1] FALSE
D43V9, continuous
D43V10, continuous
D43V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       2                         2    27
  1Q LOSS WILD-TYPE    41                        20   300
D43V12, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   2                41
  BLACK OR AFRICAN AMERICAN               2                20
  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"
D43V13, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  30
  1Q LOSS WILD-TYPE   9 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   30
  1Q LOSS WILD-TYPE    9  339
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              30               339
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    28  17
  2P LOSS WILD-TYPE 199 161
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               45               360 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               161 
$`2P LOSS MUTATED`
TCGA-BT-A20N TCGA-CU-A3KJ TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-AA77 
       26.14        18.48        46.68        50.27         9.67        20.32 
TCGA-E7-A7DU TCGA-FD-A3SJ TCGA-FD-A5BR TCGA-GC-A3YS TCGA-K4-A3WU TCGA-XF-A9SV 
        0.92        24.30        26.73        24.92         3.45        12.76 
TCGA-XF-AAMF TCGA-YF-AA3M TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-5N-A9KI TCGA-CF-A3MF 
       10.82        13.64         8.35        34.98         2.50        12.59 
TCGA-CF-A3MI TCGA-CU-A3QU TCGA-E5-A4U1 TCGA-E7-A7PW TCGA-FD-A3B5 TCGA-FJ-A3ZE 
       12.16         5.19        38.83        13.68         8.94        10.65 
TCGA-G2-A2EL TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GV-A3JV 
       26.93        66.02        15.81        14.07         0.49        14.27 
TCGA-GV-A3JW TCGA-HQ-A5NE TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-KQ-A41S TCGA-MV-A51V 
       21.34        12.16        17.72        11.80         1.15        13.48 
TCGA-S5-AA26 TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-AAMT TCGA-ZF-A9RG TCGA-ZF-A9RM 
       16.54         3.85         1.87         2.96        58.72        47.84 
TCGA-ZF-AA4X TCGA-ZF-AA5H TCGA-GU-AATO 
       67.20        29.49        10.65 

$`2P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E 
        8.98        18.58        12.92         4.90        15.12        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN 
        2.14        19.00        16.70       130.88        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       17.72        21.30        23.21        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 
       56.15        11.18        15.35        25.58         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        4.01        60.66        23.41        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS 
       19.79        12.85        27.35         3.62        15.58        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       10.78         5.69         8.25        18.08        58.92         6.28 
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-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P 
       17.62        70.32        21.40        19.13        17.75        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC 
       19.07        22.72         9.01        25.02         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
        1.84        33.14        86.83        51.32        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        13.74        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       86.30        18.58         3.88         9.63        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N 
       12.23        24.13        11.97        94.88       104.65        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.83        17.16        27.62        50.04         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 
       51.16        66.54        10.22        47.80        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         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-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        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-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.13        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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.34        11.87        13.08        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
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-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        12.03        43.59        29.72         5.36 
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-A7XN TCGA-E7-A85H 
       26.24         4.24        24.03        24.66        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-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE 
       13.35         2.27        10.85        12.66         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        48.00        15.95        59.31         7.23        20.12 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GC-A6I3 
        6.94        29.36        20.71        15.91         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
       64.01        21.24         9.07        11.70         1.81        15.42 
TCGA-K4-A83P TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
       16.27        44.38        15.32        15.58        21.07        12.23 
TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.67        38.99        17.62        37.05        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        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         6.21        45.04         6.58        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       16.27        92.98       110.60         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       27.06        75.39        18.84         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       64.08        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       56.35        35.41        19.40         8.52        54.21         5.52 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.49              0.56 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            67.20            166.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            13.68             17.88 
[1] "0.5 - 67.2 (13.7)"  "0.6 - 166.0 (17.9)"
[1] "hr=" "1.1"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         0       14        17       14
  2P LOSS WILD-TYPE       2      115       123      121
D44V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               14               115
  STAGE III              17               123
  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
  2P LOSS MUTATED         15  20   7
  2P LOSS WILD-TYPE      108 175  51
D44V4, multiclass
          clus
vv         2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1+T2              15               108
  T3                    20               175
  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
  2P LOSS MUTATED    24   4   9   1
  2P LOSS WILD-TYPE 212  43  66   7
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              24               212
  N1               4                43
  N2               9                66
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    10  35
  2P LOSS WILD-TYPE  97 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10   35
  2P LOSS WILD-TYPE   97  266
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              10                97
  MALE                35               266
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    37   4
  2P LOSS WILD-TYPE 327  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     37    4
  2P LOSS WILD-TYPE  327   16
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               37               327
  YES               4                16
[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  42
  2Q LOSS WILD-TYPE 177 136
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               92               313 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               42               136 
$`2Q LOSS MUTATED`
TCGA-BT-A20N TCGA-BT-A20T TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A2HX 
       26.14        14.89         8.98        12.92        18.48        46.68 
TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 
       50.27         9.67        17.98        64.18        67.36        36.66 
TCGA-DK-AA6R TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3SJ TCGA-FD-A3SR 
      165.73        20.32        25.58         0.92        24.30        19.79 
TCGA-FD-A5BR TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FT-A61P TCGA-GV-A3QK TCGA-K4-A3WU 
       26.73        12.36         4.31        11.08        27.35         3.45 
TCGA-K4-A4AC TCGA-KQ-A41P TCGA-UY-A78N TCGA-XF-A8HG TCGA-XF-A9SP TCGA-XF-A9SV 
        9.14        35.97        86.83        15.35        14.93        12.76 
TCGA-XF-AAMF TCGA-ZF-A9R2 TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KQ 
       10.82        21.11        34.06        57.90        24.13        94.88 
TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-5N-A9KI TCGA-BT-A20V TCGA-BT-A2LA 
        8.35        34.98         0.62         2.50         5.06        17.16 
TCGA-BT-A3PH TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A7I0 
        4.67        12.56        12.59        12.16        12.62        12.10 
TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A3IK TCGA-E5-A4U1 TCGA-E7-A7PW TCGA-E7-A97P 
        5.19        18.41         4.80        38.83        13.68        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
        8.09        16.77         8.94         5.36        27.45         2.70 
TCGA-FD-A6TF TCGA-G2-A2EL TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW 
        2.27        26.93        66.02        15.81        14.07         0.49 
TCGA-GD-A3OP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A5RJ 
        2.10        14.27        21.34        38.60        12.16        17.72 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-S5-AA26 
       11.80        44.38         1.15        15.58        13.48        16.54 
TCGA-UY-A9PD TCGA-XF-A8HH TCGA-XF-AAMG TCGA-XF-AAMT TCGA-YF-AA3L TCGA-ZF-A9R3 
       17.82         1.87       110.60         2.96        11.97        31.20 
TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4X 
       28.41        64.08        58.72        47.84        20.22        67.20 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

$`2Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A9FL 
        8.35        20.48        25.94         9.96        28.70        18.58 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
        4.90        15.12        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
      130.88        87.32         8.22        17.72        21.30        23.21 
TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       66.05        53.29        76.60        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       52.01       166.03        13.64        13.64        56.15        11.18 
TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL 
       15.35         1.22        33.04         4.01        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       17.98        29.16        46.78        12.85        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       15.58        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY 
        3.06         9.67        31.07        17.23        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       70.32        21.40        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G 
       32.78        32.98        19.82        20.28         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N 
       22.72         9.01        25.02         2.76        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH 
       50.56        46.98        14.24         1.84        33.14        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       97.45       125.49        97.12         3.22        15.98        34.45 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       66.64         2.10        13.74        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 
       86.30        18.58         3.88         9.63        13.64        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KP 
       94.29         3.48        88.87        19.69        12.23        11.97 
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y 
      104.65        44.94        16.83        17.16        27.62        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM 
       41.75        51.16        66.54        10.22        47.80        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         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-A20X TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        8.25        16.18        17.56        36.43        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S 
       23.01        12.79        13.97        12.13        13.08        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.34        11.87        13.08        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       21.86        66.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
       17.95         7.79       142.78        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       10.55       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       15.35        12.03        43.59        29.72         5.36        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-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        4.24        24.03        24.66        14.07        12.95        15.32 
TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
       32.02        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62O TCGA-FD-A62S 
       22.98        14.96        20.91        19.33         7.10        13.35 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
       10.85        12.66        10.65         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       48.00        15.95        59.31         7.23        20.12         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       29.36        20.71        15.91         8.94        13.91        26.70 
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-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3QH 
       20.05        15.78         4.73         7.00        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH 
       36.49         1.51        19.40        64.01        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT 
       11.70         1.81        15.42        16.27        15.32        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       12.23        16.67        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       76.01        78.25        69.34         3.02       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI 
       29.56         6.21         3.85        45.04         6.58        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       28.24        16.27        92.98         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        22.36        25.41 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       35.84        21.86        13.41         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5N 
        5.52 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.49              0.56 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           165.73            166.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           15.695            17.880 
[1] "0.5 - 165.7 (15.7)" "0.6 - 166.0 (17.9)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         0       29        29       33
  2Q LOSS WILD-TYPE       2      100       111      102
D45V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               29               100
  STAGE III              29               111
  STAGE IV               33               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1+T2  T3  T4
  2Q LOSS MUTATED         30  43  15
  2Q LOSS WILD-TYPE       93 152  43
D45V4, multiclass
          clus
vv         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1+T2              30                93
  T3                    43               152
  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
  2Q LOSS MUTATED    45  10  22   2
  2Q LOSS WILD-TYPE 191  37  53   6
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              45               191
  N1              10                37
  N2              22                53
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    26  66
  2Q LOSS WILD-TYPE  81 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     26   66
  2Q LOSS WILD-TYPE   81  235
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              26                81
  MALE                66               235
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    79   6
  2Q LOSS WILD-TYPE 285  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     79    6
  2Q LOSS WILD-TYPE  285   14
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               79               285
  YES               6                14
[1] 2 2
[1] FALSE
D45V9, continuous
D45V10, continuous
D45V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       9                         5    72
  2Q LOSS WILD-TYPE    34                        17   255
D45V12, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                  72               255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    24  27
  3P LOSS WILD-TYPE 203 151
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               51               354 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               27               151 
$`3P LOSS MUTATED`
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A6B5 
       28.70         8.98        12.92        18.48        16.70        50.70 
TCGA-DK-AA6R TCGA-DK-AA75 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A43Y TCGA-FD-A5C1 
      165.73        11.18         1.22        33.04        15.58        58.92 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-K4-A4AC TCGA-XF-A8HD TCGA-XF-A9T0 
       19.13        17.75        24.92         9.14        97.45        26.27 
TCGA-XF-A9T5 TCGA-XF-AAMQ TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9RE TCGA-2F-A9KR 
       66.64        71.57        86.30        13.64         3.48       104.65 
TCGA-4Z-AA7R TCGA-4Z-AA82 TCGA-BT-A20V TCGA-BT-A20X TCGA-C4-A0F0 TCGA-CF-A1HS 
       17.16        51.16         5.06         8.25         1.94        12.56 
TCGA-CF-A5UA TCGA-DK-A1A6 TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA6Q 
       12.00        66.41         7.79         8.15        10.55        13.58 
TCGA-E7-A4IJ TCGA-FD-A3B4 TCGA-FD-A3N5 TCGA-G2-A3IB TCGA-G2-AA3B TCGA-GU-A767 
       22.16        16.77        22.52         7.23        66.02         4.73 
TCGA-K4-A5RI TCGA-UY-A78O TCGA-XF-AAMT TCGA-XF-AAMW TCGA-ZF-A9RG TCGA-ZF-A9RN 
       11.70        76.01         2.96         8.32        58.72        20.22 
TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5H 
       60.16         8.52        29.49 

$`3P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       18.58         4.90        15.12        13.58         2.14        19.00 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
      130.88        46.68        87.32         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       21.30        23.21         9.67        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-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       52.01       166.03        13.64        13.64        56.15        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       15.35        25.58         0.92         4.01        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-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        8.25        18.08         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       12.69        12.36         3.06         4.31         9.67        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       17.23        11.08        33.01        17.62        70.32        21.40 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        2.76        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HE 
       14.24         1.84        33.14        86.83        51.32       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        12.76        11.90        21.04        18.90         2.24 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 
       91.73        98.99        44.32        30.94        61.45        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL 
        3.88         9.63        21.11        30.28        94.29        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W 
       94.88         8.35        44.94        16.83        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-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-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-A20U TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06        14.96        17.16        16.18         4.67        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       21.86        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY 
       17.95       142.78         4.80        13.58        20.81       163.30 
TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       15.02        18.81        19.00        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        29.72         5.36         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-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       13.68        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
       32.02         8.94        12.62        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        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-A2EO TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
       26.93        59.31        20.12         6.94        29.36        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-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV 
       18.97         7.63        20.05        15.78         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ 
       38.60        64.01        12.16        21.24         9.07        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.32        15.58        21.07        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P 
       16.54        38.99        17.62        37.05        22.68        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        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI 
        6.21         3.85        45.04         6.58         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN0 
       28.24        16.27        92.98       110.60         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       27.06        75.39        18.84         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
       64.08        47.84         2.89         8.61        59.38        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       56.35        35.41        19.40        54.21         5.52        10.65 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.22              0.49 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           165.73            166.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            17.16             17.67 
[1] "1.2 - 165.7 (17.2)" "0.5 - 166.0 (17.7)"
[1] "hr=" "1.2"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         0       13        19       19
  3P LOSS WILD-TYPE       2      116       121      116
D46V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               13               116
  STAGE III              19               121
  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
  3P LOSS MUTATED         13  25  10
  3P LOSS WILD-TYPE      110 170  48
D46V4, multiclass
          clus
vv         3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1+T2              13               110
  T3                    25               170
  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
  3P LOSS MUTATED    29   7   8   2
  3P LOSS WILD-TYPE 207  40  67   6
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              29               207
  N1               7                40
  N2               8                67
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    25   1
  3P LOSS WILD-TYPE 167  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     25    1
  3P LOSS WILD-TYPE  167   10
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              25               167
  1               1                10
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    23  28
  3P LOSS WILD-TYPE  84 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     23   28
  3P LOSS WILD-TYPE   84  273
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              23                84
  MALE                28               273
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    47   2
  3P LOSS WILD-TYPE 317  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     47    2
  3P LOSS WILD-TYPE  317   18
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               47               317
  YES               2                18
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, continuous
D46V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       3                         6    38
  3P LOSS WILD-TYPE    40                        16   289
D46V12, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   3                40
  BLACK OR AFRICAN AMERICAN               6                16
  WHITE                                  38               289
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  44
  3P LOSS WILD-TYPE   8 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   44
  3P LOSS WILD-TYPE    8  325
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              44               325
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    12  11
  3Q LOSS WILD-TYPE 215 167
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               23               382 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               11               167 
$`3Q LOSS MUTATED`
TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A6B5 TCGA-DK-AA75 TCGA-E7-A7DV TCGA-FD-A43Y 
        8.98        12.92        50.70        11.18         1.22        15.58 
TCGA-FD-A5C1 TCGA-K4-A4AC TCGA-XF-A8HD TCGA-XF-A9T0 TCGA-4Z-AA7R TCGA-C4-A0F0 
       58.92         9.14        97.45        26.27        17.16         1.94 
TCGA-CF-A5UA TCGA-DK-A3WX TCGA-DK-AA6Q TCGA-G2-A3IB TCGA-G2-AA3B TCGA-GU-A767 
       12.00        10.55        13.58         7.23        66.02         4.73 
TCGA-UY-A78O TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-AA4W TCGA-ZF-AA5H 
       76.01        28.41        58.72        60.16        29.49 

$`3Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
       28.70        18.58         4.90        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
        2.14        19.00        16.70       130.88        46.68        87.32 
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-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-AA6R TCGA-DK-AA6S 
       15.68        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        13.64        56.15        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        0.92        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       18.08         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       17.75        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
       25.02         3.45         2.76        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       51.32       125.49        97.12        15.35         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       11.31        54.90         7.63        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        9.63        13.64        21.11        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       88.87        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         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-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        17.56        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
        8.15        20.81       163.30        15.02        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.35        12.03        43.59        38.83        29.72         5.36 
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-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        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-A2EO TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
       26.93        59.31        20.12         6.94        29.36        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-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV 
       18.97         7.63        20.05        15.78         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        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-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
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        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       17.82         6.21         3.85        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
       23.64        28.24        16.27        92.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
        8.32         6.77        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       21.86        13.41        64.08        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
        8.61        59.38        67.20        56.35        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21         5.52        10.65 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.22              0.49 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            97.45            166.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            15.58             17.72 
[1] "1.2 - 97.5 (15.6)"  "0.5 - 166.0 (17.7)"
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         0        6         9        8
  3Q LOSS WILD-TYPE       2      123       131      127
D47V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II                6               123
  STAGE III               9               131
  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
  3Q LOSS MUTATED          5  13   4
  3Q LOSS WILD-TYPE      118 182  54
D47V4, multiclass
          clus
vv         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1+T2               5               118
  T3                    13               182
  T4                     4                54
[1] 3 2
[1] TRUE
[1] "dimension of 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   4   1
  3Q LOSS WILD-TYPE 221  45  71   7
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              15               221
  N1               2                45
  N2               4                71
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    10   1
  3Q LOSS WILD-TYPE 182  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     10    1
  3Q LOSS WILD-TYPE  182   10
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              10               182
  1               1                10
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     8  15
  3Q LOSS WILD-TYPE  99 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      8   15
  3Q LOSS WILD-TYPE   99  286
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               8                99
  MALE                15               286
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    21   1
  3Q LOSS WILD-TYPE 343  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     21    1
  3Q LOSS WILD-TYPE  343   19
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               21               343
  YES               1                19
[1] 2 2
[1] FALSE
D47V9, continuous
D47V10, continuous
D47V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         2    18
  3Q LOSS WILD-TYPE    42                        20   309
D47V12, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                42
  BLACK OR AFRICAN AMERICAN               2                20
  WHITE                                  18               309
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  20
  3Q LOSS WILD-TYPE   9 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   20
  3Q LOSS WILD-TYPE    9  349
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              20               349
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    70  74
  4P LOSS WILD-TYPE 157 104
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              144               261 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               74               104 
$`4P LOSS MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-CU-A0YN 
       16.77        15.12        26.14         8.35        20.48        12.92 
TCGA-CU-A0YO TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV 
        4.90        46.68        87.32         8.22        21.30         9.67 
TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA6S 
       17.98        15.68        50.70        36.66       165.73       166.03 
TCGA-DK-AA6W TCGA-E5-A4TZ TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SS 
       13.64        15.35        33.04         4.01        23.41        12.85 
TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TG TCGA-FD-A6TH 
       26.73         8.25        58.92         6.28         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-AATP 
       31.07        17.23        21.40        19.13        24.92        32.98 
TCGA-GV-A40G TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P 
       19.07        25.02         9.14        27.68        50.56        35.97 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       14.24         1.84        33.14        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAMZ 
       15.98         4.21        21.04        66.64        54.90        44.32 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-A9RE 
       61.45        86.30        18.58        13.64        94.29         3.48 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 
       19.69        57.90        24.13        17.16        27.62         0.62 
TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V 
       51.16        10.22         2.50        19.04         5.06         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 
        8.25        16.18         4.67        17.56        36.43         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI TCGA-DK-A1A7 TCGA-DK-A1AD 
       12.79        12.56        12.13        12.16        18.41       112.44 
TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-AA6Q TCGA-E7-A3X6 TCGA-E7-A4IJ 
       17.95         4.80         8.15        13.58        29.72        22.16 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A62N 
       32.02         8.94         5.52        22.98        19.33         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-G2-A3IB TCGA-G2-AA3F TCGA-GC-A3OO 
        7.10        13.35        10.85         7.23        29.36        15.81 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 
       13.91        26.70         2.20        11.31         7.63        20.05 
TCGA-GV-A3JV TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A5RJ 
       14.27        19.40        64.01        21.24        11.70        17.72 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.42        11.80         1.15        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB 
       38.99        17.62        22.68        69.34       112.83        29.56 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMT 
        6.21         3.85         6.58        23.64       110.60         2.96 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
        6.77        56.48        22.36        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA4X 
       64.08        58.72        20.22         2.89        60.16        67.20 

$`4P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A3PJ 
      108.95        16.27        33.83        12.39        14.89        25.94 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YR TCGA-CU-A3KJ 
        9.96        28.70         8.98        18.58        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IQ 
       13.58         2.14        19.00        16.70       130.88        17.72 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       50.27        23.21        66.05        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       67.36        38.24        52.01        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SJ 
       20.32        25.58         0.92         1.22        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X 
       17.98        29.16        46.78        19.79        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TA 
       15.58        53.88        10.78         5.69        18.08        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FT-A61P 
       18.81         6.15        12.69        12.36         9.67        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 
       33.01        17.62        70.32        17.75        10.92        32.78 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND 
       19.82        20.28        27.35         8.58        22.72         9.01 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-UY-A78N TCGA-UY-A9PH 
        3.45         2.76        52.73        46.98        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW 
       97.45       125.49        34.45        14.93        12.76        11.90 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       26.27        18.90         2.24         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 
       11.31         7.63        71.57        91.73        98.99        30.94 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA4R 
        3.88         9.63        21.11        30.28        88.87        34.06 
TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       12.23        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA87 
       16.83        34.98        50.04        41.75        66.54        47.80 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LA 
       13.15        12.16        17.88        19.50        14.96        17.16 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S 
       28.41        23.01        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-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AE 
        5.19        29.79         1.84        21.86        66.41        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3WW 
       17.62        15.62         7.79       142.78        13.58        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       10.55       163.30        15.02        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       12.03        43.59        38.83         5.36         2.24        16.70 
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-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-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP 
        8.09        16.77        12.62        22.52        27.98        25.74 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FJ-A3Z9 
       14.96        20.91         5.36        27.45         2.27        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-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 
       26.93        59.31        20.12        66.02         6.94        20.71 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.91        14.07         0.49         8.94         2.10         3.12 
TCGA-GD-A3OS TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW 
       20.98        18.97        15.78         4.73         7.00        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE 
       19.10         8.48        36.49         1.51        38.60        12.16 
TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 
        9.07         1.81        16.27        44.38        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       21.07        13.48        37.05        76.01        78.25         3.02 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       35.24        17.82        45.04         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        79.66        66.41         5.98        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
       92.98         8.32        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RM TCGA-ZF-AA4U 
       11.97        25.41        31.20        35.84        47.84         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       59.38        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.62              0.49 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           166.03            163.30 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            17.67             17.62 
[1] "0.6 - 166.0 (17.7)" "0.5 - 163.3 (17.6)"
[1] "hr=" "1.3"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         0       36        45       63
  4P LOSS WILD-TYPE       2       93        95       72
D48V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               36                93
  STAGE III              45                95
  STAGE IV               63                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency 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  80  19
  4P LOSS WILD-TYPE       87 115  39
D48V4, multiclass
          clus
vv         4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1+T2              36                87
  T3                    80               115
  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
  4P LOSS MUTATED    65  23  36   2
  4P LOSS WILD-TYPE 171  24  39   6
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              65               171
  N1              23                24
  N2              36                39
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    59   4
  4P LOSS WILD-TYPE 133   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     59    4
  4P LOSS WILD-TYPE  133    7
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              59               133
  1               4                 7
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    36 108
  4P LOSS WILD-TYPE  71 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     36  108
  4P LOSS WILD-TYPE   71  193
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              36                71
  MALE               108               193
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   127   6
  4P LOSS WILD-TYPE 237  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    127    6
  4P LOSS WILD-TYPE  237   14
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              127               237
  YES               6                14
[1] 2 2
[1] FALSE
D48V9, continuous
D48V10, continuous
D48V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       9                        14   116
  4P LOSS WILD-TYPE    34                         8   211
D48V12, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN              14                 8
  WHITE                                 116               211
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    70  66
  4Q LOSS WILD-TYPE 157 112
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              136               269 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               66               112 
$`4Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A2LD TCGA-CU-A0YN 
      108.95        16.77        15.12        26.14        20.48        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IT 
        4.90        15.12        46.68        87.32         8.22        21.30 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA6S 
       64.18        15.68        50.70        36.66       165.73       166.03 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL 
       15.35        25.58         0.92        33.04         4.01        23.41 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TG 
       15.58        26.73         8.25        58.92         6.28         3.06 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GU-AATP 
        4.31        31.07        17.23        21.40        19.13        32.98 
TCGA-GV-A40G TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P 
       19.07        25.02         9.14        27.68        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HF 
       46.98        14.24        33.14        86.83        51.32        97.12 
TCGA-XF-A8HG TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAN2 TCGA-XF-AAN3 
       15.35        21.04        66.64        54.90        61.45        86.30 
TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-4Z-AA7R 
       13.64        30.28        94.29         3.48        19.69        17.16 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BT-A20R TCGA-BT-A20V 
        0.62        51.16        10.22         2.50         5.06         5.06 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI TCGA-DK-A1AD TCGA-DK-A2I1 
       12.79        12.56        12.13        12.16       112.44        17.95 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-AA6Q TCGA-FD-A3B3 TCGA-FD-A3B5 
        7.79         4.80         8.15        13.58        32.02         8.94 
TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
        5.52        22.98        27.45         2.70         7.10        13.35 
TCGA-FD-A6TK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A3OO TCGA-GC-A6I3 TCGA-GD-A2C5 
       10.85        26.93         7.23        15.81        13.91        26.70 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GV-A3JV TCGA-H4-A2HQ 
        2.20        11.31         7.63        20.05        14.27        19.40 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       64.01        21.24        11.70        17.72         1.81        15.42 
TCGA-KQ-A41S TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K 
        1.15        13.48        12.23        16.67        38.99        17.62 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       22.68        69.34       112.83        29.56         6.21         3.85 
TCGA-XF-A8HC TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        6.58        23.64       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       56.48        22.36        21.86        13.41        64.08        58.72 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA54 
       20.22         2.89        67.20        19.40 

$`4Q LOSS WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ 
       16.27        33.83        12.39        14.89         8.35        25.94 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A3KJ TCGA-CU-A72E 
        9.96        28.70         8.98        18.58        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.14        19.00        16.70       130.88        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21         9.67        66.05        17.98        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       67.36        38.24        52.01        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
       11.18        20.32         1.22        60.66        24.30        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB 
       53.88        10.78         5.69        18.08        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FT-A61P TCGA-G2-A2ES 
        6.15        12.69        12.36         9.67        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       17.62        70.32        17.75        24.92        10.92        32.78 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND 
       19.82        20.28        27.35         8.58        22.72         9.01 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41N TCGA-S5-A6DX TCGA-XF-A8HD TCGA-XF-A8HE 
        3.45         2.76        52.73         1.84        97.45       125.49 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 
       11.90        26.27        18.90         2.24         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       10.82        11.31         7.63        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 
       44.32        30.94        18.58         3.88         9.63        21.11 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       88.87        34.06        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KM 
       27.62        50.04        41.75        66.54        47.80        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X 
       19.04        12.16        17.88        19.50        14.96         8.25 
TCGA-BT-A2LA TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S 
       17.16        23.01        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-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3WW 
       16.14        17.62        15.62       142.78        13.58        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       10.55       163.30        15.02        18.81        19.00        15.35 
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         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        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-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       27.98        25.74        14.96        20.91        19.33         5.36 
TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
        2.27        12.66        10.65         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       48.00        15.95        59.31        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       29.36        20.71        15.91        14.07         0.49         8.94 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-A767 
        2.10         3.12        20.98        18.97        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
        7.00        21.34        19.10         8.48        36.49         1.51 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       38.60        12.16         9.07        16.27        11.80        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78O 
       15.32        15.58        21.07        16.54        37.05        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HH 
       78.25         3.02        35.24        17.82        45.04         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
       28.24        16.27        92.98        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
        0.66        11.97        25.41        31.20        35.84        28.41 
TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
       47.84         8.61        59.38        60.16        56.35        35.41 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21        29.49         5.52        10.65 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.62              0.49 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           166.03            163.30 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            17.67             17.62 
[1] "0.6 - 166.0 (17.7)" "0.5 - 163.3 (17.6)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         0       33        47       56
  4Q LOSS WILD-TYPE       2       96        93       79
D49V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               33                96
  STAGE III              47                93
  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         36  73  18
  4Q LOSS WILD-TYPE       87 122  40
D49V4, multiclass
          clus
vv         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1+T2              36                87
  T3                    73               122
  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
  4Q LOSS MUTATED    67  21  30   2
  4Q LOSS WILD-TYPE 169  26  45   6
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              67               169
  N1              21                26
  N2              30                45
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    55   4
  4Q LOSS WILD-TYPE 137   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     55    4
  4Q LOSS WILD-TYPE  137    7
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              55               137
  1               4                 7
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    38  98
  4Q LOSS WILD-TYPE  69 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     38   98
  4Q LOSS WILD-TYPE   69  203
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              38                69
  MALE                98               203
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   120   5
  4Q LOSS WILD-TYPE 244  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    120    5
  4Q LOSS WILD-TYPE  244   15
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              120               244
  YES               5                15
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, continuous
D49V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       9                        12   110
  4Q LOSS WILD-TYPE    34                        10   217
D49V12, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   9                34
  BLACK OR AFRICAN AMERICAN              12                10
  WHITE                                 110               217
[1] 3 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    28  25
  5P LOSS WILD-TYPE 199 153
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               53               352 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               25               153 
$`5P LOSS MUTATED`
TCGA-4Z-AA7Q TCGA-BT-A2LD TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-AA75 
       16.77        20.48        50.27        21.30        66.05        11.18 
TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-G2-A3VY TCGA-GV-A6ZA 
        0.92        33.04        24.30        23.41        17.62        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41P TCGA-R3-A69X 
        9.01         3.45         2.76        52.73        35.97        14.24 
TCGA-XF-A8HG TCGA-XF-A9SV TCGA-XF-AAMZ TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7R 
       15.35        12.76        44.32        24.13         8.35        17.16 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A2LB TCGA-BT-A3PH TCGA-C4-A0F6 TCGA-CF-A1HR 
        6.58        19.04        16.18         4.67        23.01        12.79 
TCGA-CF-A3MI TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IM 
       12.16        18.41       112.44        17.95        13.58         8.15 
TCGA-E5-A2PC TCGA-E7-A6ME TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FJ-A3ZE TCGA-G2-A2EF 
       43.59        24.03        20.91        27.45        10.65        61.94 
TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GV-A3JW TCGA-K4-A3WV TCGA-UY-A8OD TCGA-UY-A9PD 
        8.94         2.20        21.34        21.24       112.83        17.82 
TCGA-UY-A9PF TCGA-XF-A9SI TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-ZF-A9R0 
        3.85        79.66         6.77        56.48        22.36 

$`5P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
       14.89         8.35        25.94         9.96        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
       18.58        12.92         4.90        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
        2.14        19.00        16.70       130.88        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV 
        8.22        17.72        23.21         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B7 
       56.15        20.32        15.35        25.58         1.22         4.01 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       60.66        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35         3.62        15.58        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
        5.69         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D 
        9.67        31.07        17.23        11.08        33.01        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-S5-A6DX 
       25.02         9.14        27.68        50.56        46.98         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       33.14        86.83        51.32        97.45       125.49        97.12 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW 
        3.22        15.98        34.45        14.93         4.21        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       91.73        98.99        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       11.97        94.88       104.65        44.94        16.83        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-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-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        2.66         6.74        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42B 
        5.06        14.96         5.06         8.25        17.16        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
       36.43        28.41         1.94        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.13        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       21.86        66.41        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
      142.78         4.80        20.81        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
       13.58        18.81        19.00        15.35        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        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-A7PW 
        0.66        26.96        26.24         4.24        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N 
       25.74        22.98        14.96        19.33         5.36         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 
        7.10        13.35         2.27        10.85        12.66         8.94 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
        3.25        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         0.49        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        3.12        20.98        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH 
       15.78         4.73         7.00        14.27        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
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-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       11.80        44.38         1.15        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       13.48        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        22.68        76.01        78.25        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       35.24        29.56         6.21        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       17.88        48.62        64.80        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       28.24        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        11.97        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.92              0.49 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           112.83            166.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            18.41             17.49 
[1] "0.9 - 112.8 (18.4)" "0.5 - 166.0 (17.5)"
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         0       14        20       20
  5P LOSS WILD-TYPE       2      115       120      115
D50V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               14               115
  STAGE III              20               120
  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
  5P LOSS MUTATED         14  29   8
  5P LOSS WILD-TYPE      109 166  50
D50V4, multiclass
          clus
vv         5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1+T2              14               109
  T3                    29               166
  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
  5P LOSS MUTATED    30   5  11   3
  5P LOSS WILD-TYPE 206  42  64   5
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              30               206
  N1               5                42
  N2              11                64
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    25   4
  5P LOSS WILD-TYPE 167   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     25    4
  5P LOSS WILD-TYPE  167    7
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              25               167
  1               4                 7
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    16  38
  5P LOSS WILD-TYPE  91 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     16   38
  5P LOSS WILD-TYPE   91  263
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              16                91
  MALE                38               263
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    49   2
  5P LOSS WILD-TYPE 315  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     49    2
  5P LOSS WILD-TYPE  315   18
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               49               315
  YES               2                18
[1] 2 2
[1] FALSE
D50V9, continuous
D50V10, continuous
D50V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       5                         4    43
  5P LOSS WILD-TYPE    38                        18   284
D50V12, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   5                38
  BLACK OR AFRICAN AMERICAN               4                18
  WHITE                                  43               284
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1  48
  5P LOSS WILD-TYPE   8 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   48
  5P LOSS WILD-TYPE    8  321
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 8
  NOT HISPANIC OR LATINO              48               321
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    83  76
  5Q LOSS WILD-TYPE 144 102
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              159               246 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               76               102 
$`5Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-DK-A1A5 TCGA-DK-A3IN 
      108.95        16.77        20.48        25.94         2.14         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6AV 
       17.72        50.27        21.30        23.21        66.05        64.18 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 
       15.68        50.70       165.73       166.03        13.64        11.18 
TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       15.35         0.92        33.04        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C0 
       29.16        19.79        12.85        26.73         8.25        18.08 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FJ-A3ZF 
       62.86        18.81         6.15        12.69         3.06        17.23 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.08        17.62        10.92        32.98        19.82        20.28 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       19.07        22.72         9.01         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV 
       97.12        15.35        15.98        34.45        14.93        12.76 
TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9RC 
        2.24        54.90         7.63        18.58        13.64        94.29 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-2F-A9KP TCGA-4Z-AA7O 
       88.87        34.06        19.69        24.13        11.97        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA86 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20R 
       17.16        27.62        10.22         6.58        19.04         5.06 
TCGA-BT-A20V TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR 
        5.06         4.67        17.56        36.43        23.01        12.79 
TCGA-CF-A3MH TCGA-CU-A3QU TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IM 
       13.08         5.19       112.44        17.95        13.58         8.15 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 
       15.02        13.58        19.00        12.03        43.59        29.72 
TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3N5 
       22.16        24.03        13.68         8.09         8.94        22.52 
TCGA-FD-A3SP TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S 
       25.74        20.91         5.36        27.45         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A3IB TCGA-G2-A3IE 
        2.27        10.85        10.65        61.94         7.23        20.12 
TCGA-G2-AA3B TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       66.02         0.49         8.94        13.91        26.70         2.10 
TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HQ 
        2.20         7.63         7.00        21.34        19.10        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-KQ-A41R TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K 
       64.01        12.16        44.38        16.67        38.99        17.62 
TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        78.25        69.34       112.83        29.56        17.82 
TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A9SI TCGA-XF-A9SZ TCGA-XF-AAMT TCGA-XF-AAMX 
        3.85         6.58        79.66        28.24         2.96         6.77 
TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 
       56.48        11.97        22.36        25.41        31.20        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA51 
       28.41        47.84        20.22         2.89        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA5H TCGA-GU-AATO 
       35.41        29.49        10.65 

$`5Q LOSS WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
       16.27        15.12        33.83        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN 
        8.35         9.96        28.70         8.98        18.58        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB 
        4.90        15.12        18.48        13.58        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW 
      130.88        46.68        87.32         9.67        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA71 
       76.60        67.36        36.66        38.24        52.01        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA 
       56.15        20.32        25.58         1.22         4.01        60.66 
TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       46.78        27.35         3.62        15.58        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI 
        5.69        58.92         6.28        12.36         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       31.07        33.01        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A40E TCGA-K4-A3WS TCGA-S5-A6DX 
       24.92        32.78        27.35         8.58        25.02         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SJ 
       33.14        86.83        51.32        97.45       125.49         3.22 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 
        4.21        11.90        21.04        26.27        18.90        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.10        13.74        10.82        11.31        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 
       98.99        44.32        30.94        61.45        86.30         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-AA53 TCGA-ZF-AA5P 
        9.63        21.11        30.28         3.48        57.90        12.23 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       94.88       104.65         8.35        44.94        34.98        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KI 
        0.62        41.75        51.16        66.54        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX 
       17.42        40.08         7.33         2.66         6.74        13.15 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA 
       12.16        17.88        19.50        14.96         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
       16.18        28.41         1.94        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-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.34        11.87        13.08        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       66.41        18.41        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6T 
      142.78         4.80        20.81        10.55       163.30        18.81 
TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       15.35        38.83         5.36         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN 
        0.66        26.96        26.24         4.24        24.66        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 
       12.95        15.32        14.37        32.02        16.77        12.62 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62N 
       27.98         5.52        22.98        14.96        19.33         2.70 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       12.66         8.94         3.25        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       59.31         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 
       14.07         3.12        20.98        11.31        18.97        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       15.78         4.73        14.27         8.48        36.49         1.51 
TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       38.60        21.24         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-AA26 TCGA-UY-A78L TCGA-UY-A78O 
       21.07        13.48        12.23        16.54        37.05        76.01 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI 
        3.02        35.24         6.21        45.04         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 
       48.62        64.80        66.41         5.98        23.64        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
       92.98       110.60         8.32        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4U 
        0.66        35.84        13.41        64.08        58.72         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       59.38        60.16        19.40         8.52        54.21         5.52 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.49              0.56 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           166.03            163.30 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           18.810            16.405 
[1] "0.5 - 166.0 (18.8)" "0.6 - 163.3 (16.4)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         0       45        50       65
  5Q LOSS WILD-TYPE       2       84        90       70
D51V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               45                84
  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         41  82  23
  5Q LOSS WILD-TYPE       82 113  35
D51V4, multiclass
          clus
vv         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1+T2              41                82
  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    77  21  36   6
  5Q LOSS WILD-TYPE 159  26  39   2
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              77               159
  N1              21                26
  N2              36                39
  N3               6                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    66   7
  5Q LOSS WILD-TYPE 126   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     66    7
  5Q LOSS WILD-TYPE  126    4
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              66               126
  1               7                 4
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    41 119
  5Q LOSS WILD-TYPE  66 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     41  119
  5Q LOSS WILD-TYPE   66  182
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              41                66
  MALE               119               182
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   142   8
  5Q LOSS WILD-TYPE 222  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    142    8
  5Q LOSS WILD-TYPE  222   12
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO              142               222
  YES               8                12
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, continuous
D51V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED      11                        13   129
  5Q LOSS WILD-TYPE    32                         9   198
D51V12, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                  11                32
  BLACK OR AFRICAN AMERICAN              13                 9
  WHITE                                 129               198
[1] 3 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     4 145
  5Q LOSS WILD-TYPE   5 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4  145
  5Q LOSS WILD-TYPE    5  224
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             145               224
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    64  39
  6P LOSS WILD-TYPE 163 139
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              103               302 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               39               139 
$`6P LOSS MUTATED`
TCGA-2F-A9KT TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A42C TCGA-DK-A1AB TCGA-DK-A2HX 
      108.95        26.14        20.48        28.70        16.70        46.68 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 
       17.72        50.27        21.30        17.98        64.18        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-E5-A4TZ 
       36.66       165.73       166.03        13.64        13.64        15.35 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43Y TCGA-FD-A6TE TCGA-FJ-A3Z7 
       23.41        29.16        46.78        15.58        12.36        31.07 
TCGA-FJ-A3ZF TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GV-A3JZ TCGA-K4-A4AB TCGA-KQ-A41N 
       17.23        70.32        19.13        19.82         2.76        52.73 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-XF-A8HG TCGA-XF-A9SM TCGA-XF-A9SP 
       35.97        46.98        14.24        15.35        34.45        14.93 
TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R2 
        2.24        54.90        44.32        86.30        13.64        21.11 
TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA82 
       57.90        24.13         8.35        17.16        27.62        51.16 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-CF-A1HR TCGA-CF-A3MG 
        5.06         8.25        16.18         4.67        12.79        12.13 
TCGA-CF-A3MI TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-AA6P 
       12.16         5.19         1.84       142.78        13.58        15.02 
TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A7PW TCGA-E7-A97Q 
       19.00        12.03        38.83         0.56        13.68         8.09 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62O TCGA-G2-A2EO TCGA-G2-A3IE 
       20.91        19.33         5.36         7.10        59.31        20.12 
TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3QI 
       29.36        14.07         2.10         4.73        21.34        36.49 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41R 
       19.40        38.60        64.01        11.70         1.81        44.38 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A8OD TCGA-XF-A8HH 
       13.48        16.67        38.99        17.62       112.83         1.87 
TCGA-XF-A9SG TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YF-AA3L 
       48.62       110.60         8.32        56.48        75.39        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA4N TCGA-ZF-AA51 
       22.36        25.41        21.86        28.41         2.89        56.35 
TCGA-ZF-AA5H 
       29.49 

$`6P LOSS WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T 
       16.27        16.77        15.12        33.83        12.39        14.89 
TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN 
        8.35        25.94         9.96         8.98        18.58        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
        4.90        15.12        18.48        13.58         2.14        19.00 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
      130.88        87.32         8.22        23.21         9.67        66.05 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6M 
       53.29        76.60        67.36        15.68        38.24        52.01 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       56.15        11.18        20.32        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SR 
       33.04         4.01        60.66        24.30        17.98        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
        5.69         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       18.81         6.15        12.69         3.06         4.31         9.67 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A3YS 
       11.08        33.01        17.62        21.40        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       10.92        32.78        32.98        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC 
       19.07        22.72         9.01        25.02         3.45         9.14 
TCGA-K4-A54R TCGA-KQ-A41O TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       27.68        50.56         1.84        33.14        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST 
       97.45       125.49        97.12         3.22        15.98         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 
       12.76        11.90        21.04        26.27        18.90        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ 
        2.10        13.74        10.82        11.31         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 
       91.73        98.99        30.94        61.45        18.58         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
        9.63        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N 
       19.69        12.23        11.97        94.88       104.65        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 
       16.83        34.98        50.04         0.62        41.75        66.54 
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-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A42B 
       17.88        19.50         5.06        14.96        17.16        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C 
       36.43        28.41         1.94        23.01        12.56        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-A9FM TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 
       11.34        11.87        13.08        29.79        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        7.79         4.80         8.15        20.81        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.58        18.81        15.35        43.59        29.72         5.36 
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-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        4.24        24.03        24.66        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BZ 
       27.98         5.52        25.74        22.98        14.96        27.45 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.70        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
        7.23        66.02         6.94        20.71        15.81        15.91 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
        0.49         8.94        13.91        26.70         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HO TCGA-HQ-A5NE 
        7.00        14.27        19.10         8.48         1.51        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       21.24         9.07        17.72        15.42        16.27        11.80 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 
        1.15        15.32        15.58        21.07        12.23        16.54 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        22.68        76.01        78.25        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       35.24        29.56        17.82         6.21         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
        6.58        17.88        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMX 
       23.64        28.24        16.27        92.98         2.96         6.77 
TCGA-XF-AAN4 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RD 
       27.06        18.84         0.66        31.20        35.84        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V 
       64.08        58.72        47.84        20.22         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        67.20        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.56              0.49 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           166.03            163.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           20.120            16.735 
[1] "0.6 - 166.0 (20.1)" "0.5 - 163.3 (16.7)"
[1] "hr=" "1.4"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         0       28        35       39
  6P LOSS WILD-TYPE       2      101       105       96
D52V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               28               101
  STAGE III              35               105
  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         24  49  19
  6P LOSS WILD-TYPE       99 146  39
D52V4, multiclass
          clus
vv         6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1+T2              24                99
  T3                    49               146
  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    55   7  27   3
  6P LOSS WILD-TYPE 181  40  48   5
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              55               181
  N1               7                40
  N2              27                48
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    32  71
  6P LOSS WILD-TYPE  75 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     32   71
  6P LOSS WILD-TYPE   75  230
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              32                75
  MALE                71               230
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    94   4
  6P LOSS WILD-TYPE 270  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     94    4
  6P LOSS WILD-TYPE  270   16
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               94               270
  YES               4                16
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, continuous
D52V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       7                         7    82
  6P LOSS WILD-TYPE    36                        15   245
D52V12, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   7                36
  BLACK OR AFRICAN AMERICAN               7                15
  WHITE                                  82               245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  92
  6P LOSS WILD-TYPE   4 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   92
  6P LOSS WILD-TYPE    4  277
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 4
  NOT HISPANIC OR LATINO              92               277
[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 139 107
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              159               246 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               71               107 
$`6Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A42C TCGA-DK-A1AB 
      108.95        16.27        26.14        20.48        28.70        16.70 
TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV 
       46.68        17.72        50.27        21.30        17.98        64.18 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       50.70        36.66        38.24       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ 
       13.64        15.35         1.22        23.41        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P 
       19.79        15.58        26.73         8.25        18.08         6.28 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.15        12.36         3.06         4.31        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GU-AATP TCGA-GV-A3JZ 
       11.08        33.01        70.32        19.13        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
       20.28        22.72         2.76        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       46.98        14.24        33.14        15.35         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 
       34.45        14.93         4.21        11.90        26.27         2.24 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3M 
       54.90         7.63        91.73        44.32        86.30        13.64 
TCGA-ZF-A9R2 TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7R 
       21.11        34.06        57.90        24.13         8.35        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-BT-A20V 
       27.62         0.62        41.75        51.16        10.22         5.06 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CF-A3MI 
       16.18         4.67         1.94        12.79        12.13        12.16 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
        5.19         1.84        66.41        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
        4.80        13.58        15.02        13.58        18.81        19.00 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD 
       12.03        43.59        38.83        22.16         0.56         4.24 
TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       13.68         8.09         8.94        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B 
       27.45         7.10        13.35        59.31        20.12        66.02 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GU-A42R 
       29.36        20.71        14.07         8.94         2.10        18.97 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        7.63         4.73         7.00        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A6FZ 
       36.49        19.40        38.60        64.01        11.70         1.81 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K 
       44.38        15.58        13.48        16.67        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-A8HH TCGA-XF-A9SG TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN5 
        1.87        48.62       110.60         8.32        56.48        75.39 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA4N 
       11.97        22.36        25.41        21.86        28.41         2.89 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA5H 
       56.35        35.41        29.49 

$`6Q LOSS WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W 
       16.77        15.12        33.83        12.39        14.89         8.35 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       25.94         9.96         8.98        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC 
       15.12        18.48        13.58         2.14        19.00       130.88 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AW 
       87.32         8.22        23.21         9.67        66.05        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6M TCGA-DK-AA74 TCGA-DK-AA75 
       76.60        67.36        15.68        52.01        56.15        11.18 
TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       20.32        25.58         0.92        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS 
       24.30        17.98        12.85        27.35         3.62        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
       10.78         5.69        58.92        62.86        18.81        12.69 
TCGA-FD-A6TI TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
        9.67        17.62        21.40        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS 
       32.78        27.35         8.58        19.07         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-S5-A6DX TCGA-UY-A78N TCGA-UY-A9PH 
        3.45         9.14        27.68         1.84        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T2 
       97.45       125.49        97.12        12.76        21.04        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMQ 
       66.64         2.10        13.74        10.82        11.31        71.57 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       98.99        30.94        61.45        18.58         3.88         9.63 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA5P 
       30.28        94.29         3.48        88.87        19.69        12.23 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       11.97        94.88       104.65        44.94        16.83        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       50.04        66.54        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X 
       12.16        17.88        19.50         5.06        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS 
       17.16        17.56        36.43        28.41        23.01        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       13.97        12.59        13.08        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-DK-A1A3 
       11.34        11.34        11.87        13.08        29.79        21.86 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IM 
       18.41       112.44        16.14        17.62        15.62         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6X TCGA-E7-A3X6 TCGA-E7-A3Y1 
       20.81        10.55       163.30        15.35        29.72         5.36 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        2.24        16.70         0.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
       16.77        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A62N TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
       22.98        14.96         2.70         2.27        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-AA3C TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A4ZW 
       26.93         7.23         6.94        15.81        15.91         0.49 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       13.91        26.70         3.12        20.98         2.20        11.31 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WV 
       20.05        15.78        14.27         1.51        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S 
        9.07        17.72        15.42        16.27        11.80         1.15 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78O 
       15.32        21.07        12.23        16.54        37.05        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC 
       78.25         3.02        35.24        17.82         6.21         6.58 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       17.88        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN4 
       28.24        16.27        92.98         2.96         6.77        27.06 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       18.84         0.66        31.20        35.84        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       58.72        47.84        20.22         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       67.20        19.40         8.52        54.21         5.52        10.65 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.56              0.49 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           166.03            163.30 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            19.13             16.62 
[1] "0.6 - 166.0 (19.1)" "0.5 - 163.3 (16.6)"
[1] "hr=" "1"  
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         0       44        47       67
  6Q LOSS WILD-TYPE       2       85        93       68
D53V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               44                85
  STAGE III              47                93
  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
  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    79  20  40   5
  6Q LOSS WILD-TYPE 157  27  35   3
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              79               157
  N1              20                27
  N2              40                35
  N3               5                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    73   3
  6Q LOSS WILD-TYPE 119   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     73    3
  6Q LOSS WILD-TYPE  119    8
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              73               119
  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   145   5
  6Q LOSS WILD-TYPE 219  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    145    5
  6Q LOSS WILD-TYPE  219   15
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO              145               219
  YES               5                15
[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     7 139
  6Q LOSS WILD-TYPE   2 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7  139
  6Q LOSS WILD-TYPE    2  230
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                 2
  NOT HISPANIC OR LATINO             139               230
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     9  10
  7P LOSS WILD-TYPE 218 168
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               19               386 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               10               168 
$`7P LOSS MUTATED`
TCGA-DK-A1A5 TCGA-DK-A6B5 TCGA-DK-AA6W TCGA-DK-AA77 TCGA-FD-A5BY TCGA-FD-A6TA 
        2.14        50.70        13.64        20.32         8.25        62.86 
TCGA-GV-A3QF TCGA-K4-A3WS TCGA-KQ-A41Q TCGA-XF-AAML TCGA-XF-AAMZ TCGA-ZF-A9RL 
       20.28        25.02        46.98         7.63        44.32        88.87 
TCGA-ZF-AA4T TCGA-4Z-AA7S TCGA-BT-A20X TCGA-CF-A47X TCGA-ZF-AA54 TCGA-ZF-AA58 
       19.69        34.98         8.25        12.62        19.40        54.21 
TCGA-GU-AATO 
       10.65 

$`7P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       28.70         8.98        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       18.48        13.58        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       67.36        15.68        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 
      166.03        13.64        56.15        11.18        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        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-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35         3.62        15.58        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC 
        5.69        18.08        58.92         6.28        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       12.69        12.36         3.06         4.31         9.67        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       17.23        11.08        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       19.13        17.75        24.92        10.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       19.82        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       35.97        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       97.45       125.49        97.12        15.35         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       10.82        11.31        54.90        71.57        91.73        98.99 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R 
       13.64        21.11        30.28        94.29         3.48        34.06 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y 
        8.35        44.94        16.83        17.16        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
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-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-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-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        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-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
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-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
      142.78         4.80        13.58         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
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         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       14.96        20.91        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       20.71        15.81        15.91        14.07         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
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-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
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-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       11.80        44.38         1.15        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       13.48        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        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        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       45.04         6.58         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       27.06        75.39        18.84         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 
       59.38        60.16        67.20        56.35        35.41         8.52 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       29.49         5.52 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             2.14              0.49 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            88.87            166.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            20.28             17.59 
[1] "2.1 - 88.9 (20.3)"  "0.5 - 166.0 (17.6)"
[1] "hr=" "1.1"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED         0        6         5        9
  7P LOSS WILD-TYPE       2      123       135      126
D54V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 0                 2
  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          5   9   5
  7P LOSS WILD-TYPE      118 186  53
D54V4, multiclass
          clus
vv         7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1+T2               5               118
  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 227  47  67   7
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               9               227
  N1               0                47
  N2               8                67
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     7   0
  7P LOSS WILD-TYPE 185  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    0
  7P LOSS WILD-TYPE  185   11
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               7               185
  1               0                11
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3  17
  7P LOSS WILD-TYPE 104 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3   17
  7P LOSS WILD-TYPE  104  284
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3               104
  MALE                17               284
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    16   2
  7P LOSS WILD-TYPE 348  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     16    2
  7P LOSS WILD-TYPE  348   18
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               16               348
  YES               2                18
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, continuous
D54V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         1    18
  7P LOSS WILD-TYPE    42                        21   309
D54V12, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                42
  BLACK OR AFRICAN AMERICAN               1                21
  WHITE                                  18               309
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  19
  7P LOSS WILD-TYPE   9 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   19
  7P LOSS WILD-TYPE    9  350
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              19               350
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    16  12
  7Q LOSS WILD-TYPE 211 166
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               28               377 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               12               166 
$`7Q LOSS MUTATED`
TCGA-DK-A1A5 TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-K4-A3WS TCGA-KQ-A41Q 
        2.14         8.25        18.08        12.36        25.02        46.98 
TCGA-XF-A9SM TCGA-XF-AAML TCGA-XF-AAMZ TCGA-YF-AA3M TCGA-ZF-A9RL TCGA-ZF-AA4T 
       34.45         7.63        44.32        13.64        88.87        19.69 
TCGA-4Z-AA7S TCGA-BT-A20X TCGA-CF-A47X TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
       34.98         8.25        12.62       142.78         4.80         8.15 
TCGA-DK-AA6P TCGA-E7-A6ME TCGA-GC-A4ZW TCGA-GU-A766 TCGA-GU-AATQ TCGA-K4-A5RH 
       15.02        24.03         0.49        15.78         7.00         9.07 
TCGA-UY-A8OB TCGA-XF-AAMT TCGA-ZF-A9RF TCGA-GU-AATO 
       69.34         2.96        64.08        10.65 

$`7Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       28.70         8.98        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       18.48        13.58        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y 
       46.78        19.79        12.85        27.35         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62P 
       26.73        53.88        10.78         5.69        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH 
       62.86        18.81         6.15        12.69         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        9.67        31.07        17.23        11.08        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       70.32        21.40        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       19.07        22.72         9.01         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX 
       27.68        52.73        50.56        35.97        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       33.14        86.83        51.32        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
       15.35         3.22        15.98        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
        2.10        13.74        10.82        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       91.73        98.99        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        3.88         9.63        21.11        30.28        94.29         3.48 
TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       34.06        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W 
      104.65         8.35        44.94        16.83        17.16        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         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-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB 
       19.50         5.06        14.96         5.06        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        17.56        36.43        28.41         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-A47Y 
       12.16        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q 
        7.79        13.58        20.81        10.55       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        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-A7PW 
        0.66        26.96        26.24         4.24        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A767 
        2.20        11.31        18.97         7.63        20.05         4.73 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI 
       19.40        38.60        64.01        12.16        21.24        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        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-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       76.01        78.25         3.02       112.83        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       17.82         6.21         3.85        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW 
       23.64        28.24        16.27        92.98       110.60         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        6.77        56.48        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       28.41        13.41        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       19.40         8.52        54.21        29.49         5.52 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.49              0.56 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           142.78            166.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            14.33             17.72 
[1] "0.5 - 142.8 (14.3)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED         0        9        10        9
  7Q LOSS WILD-TYPE       2      120       130      126
D55V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II                9               120
  STAGE III              10               130
  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          7  15   4
  7Q LOSS WILD-TYPE      116 180  54
D55V4, multiclass
          clus
vv         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1+T2               7               116
  T3                    15               180
  T4                     4                54
[1] 3 2
[1] TRUE
[1] "dimension of 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    15   1   8   0
  7Q LOSS WILD-TYPE 221  46  67   8
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              15               221
  N1               1                46
  N2               8                67
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    11   0
  7Q LOSS WILD-TYPE 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  24
  7Q LOSS WILD-TYPE 103 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4   24
  7Q LOSS WILD-TYPE  103  277
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               4               103
  MALE                24               277
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    23   1
  7Q LOSS WILD-TYPE 341  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     23    1
  7Q LOSS WILD-TYPE  341   19
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               23               341
  YES               1                19
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, continuous
D55V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       2                         1    24
  7Q LOSS WILD-TYPE    41                        21   303
D55V12, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   2                41
  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"
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  77
  8P LOSS WILD-TYPE 118 101
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              186               219 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               77               101 
$`8P LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-BT-A20W TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
      108.95        16.77         8.35         9.96        28.70         8.98 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       12.92        18.48       130.88        46.68        87.32         8.22 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       21.30         9.67        64.18        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       52.01       166.03        13.64        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ 
       25.58         0.92         1.22        33.04         4.01        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR 
       23.41        17.98        19.79        27.35        15.58        26.73 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE 
        8.25        18.08         6.28        62.86        12.69        12.36 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-AA3D TCGA-GC-A3RB 
        4.31        31.07        17.23        11.08        70.32        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.75        24.92        10.92        32.98        19.82        20.28 
TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        8.58        19.07         9.01        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 
        9.14        27.68        52.73        46.98        14.24        33.14 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV 
       51.32         3.22        15.98        34.45         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAML 
       11.90        26.27         2.24        66.64        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAN2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       71.57        61.45        30.28         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR 
       19.69        57.90        12.23        24.13        11.97       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA86 TCGA-5N-A9KI 
        8.35        17.16        27.62         0.62        10.22         2.50 
TCGA-BL-A13J TCGA-BT-A2LB TCGA-BT-A42F TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A8HX 
        2.66        16.18        28.41        12.56        10.95        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD 
       11.34        11.87         5.19        21.86        18.41       112.44 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6U TCGA-DK-AA76 
      142.78         4.80        13.58         8.15        19.00        12.03 
TCGA-E5-A4U1 TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A7PW TCGA-FD-A3B4 TCGA-FD-A3B5 
       38.83        26.96         4.24        13.68        16.77         8.94 
TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N 
       22.52         5.52        22.98        19.33        27.45         2.70 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-AA3C 
        2.27        10.85        61.94        15.95        20.12         6.94 
TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       29.36        15.91        14.07         0.49        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JW 
        2.10         3.12         7.63        20.05        15.78        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.10         8.48        19.40        12.16        21.24         9.07 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R 
       17.72         1.81        15.42        11.80        44.38        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78L 
       15.58        21.07        12.23        16.67        17.62        37.05 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC 
       69.34       112.83        29.56        17.82        45.04         6.58 
TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
        1.87        79.66       110.60         2.96         8.32        56.48 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9RD TCGA-ZF-AA4U 
       75.39        18.84        22.36        25.41        13.41         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       59.38        60.16         8.52        54.21        29.49        10.65 

$`8P LOSS WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
       16.27        15.12        33.83        12.39        26.14        14.89 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E 
       20.48        25.94        18.58         4.90        15.12        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
        2.14        19.00        16.70        17.72        50.27        23.21 
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-AA6R TCGA-DK-AA71 TCGA-DK-AA74 TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SQ 
      165.73        13.64        56.15        60.66        29.16        46.78 
TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 
       12.85         3.62        53.88        10.78         5.69        58.92 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-G2-A2ES TCGA-G2-A3VY 
       18.81         6.15         3.06         9.67        33.01        17.62 
TCGA-GC-A3BM TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-KQ-A41O TCGA-KQ-A41P 
       21.40        32.78        27.35        22.72        50.56        35.97 
TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        1.84        86.83        97.45       125.49        97.12        15.35 
TCGA-XF-A9SP TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       14.93        21.04        18.90         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 
       11.31        91.73        98.99        44.32        30.94        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC 
       18.58         3.88         9.63        13.64        21.11        94.29 
TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 
       94.88        44.94        16.83        34.98        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       51.16        66.54        47.80        17.42        40.08         7.33 
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-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        4.67        17.56        36.43         1.94        23.01        12.79 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47T 
       13.97        12.59        12.13        13.08        12.16        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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AE 
       12.10        13.08        29.79         1.84        66.41        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3WW TCGA-DK-A3WX 
       17.62        15.62        17.95         7.79        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E5-A2PC 
      163.30        15.02        13.58        18.81        15.35        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H 
        0.66        26.24        24.03        24.66        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 
       15.32        14.37         8.09        32.02        12.62        27.98 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A62S 
       25.74        14.96        20.91         5.36         7.10        13.35 
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-A3IB TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 
       59.31         7.23        66.02        20.71        15.81         8.94 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ 
       20.98         2.20        11.31        18.97         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI 
       14.27        36.49         1.51        38.60        64.01        11.70 
TCGA-K4-A83P TCGA-KQ-A41S TCGA-MV-A51V TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78M 
       16.27         1.15        13.48        16.54        38.99        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF 
       76.01        78.25         3.02        35.24         6.21         3.85 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       17.88        48.62        64.80        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-YC-A9TC 
       28.24        16.27        92.98         6.77        27.06         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF 
       11.97        31.20        35.84        21.86        28.41        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        67.20        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              0.56 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           166.03            165.73 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            17.67             17.62 
[1] "0.5 - 166.0 (17.7)" "0.6 - 165.7 (17.6)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         0       57        55       76
  8P LOSS WILD-TYPE       2       72        85       59
D56V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               57                72
  STAGE III              55                85
  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
  8P LOSS MUTATED         51  91  29
  8P LOSS WILD-TYPE       72 104  29
D56V4, multiclass
          clus
vv         8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1+T2              51                72
  T3                    91               104
  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
  8P LOSS MUTATED    98  27  43   3
  8P LOSS WILD-TYPE 138  20  32   5
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              98               138
  N1              27                20
  N2              43                32
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    46 142
  8P LOSS WILD-TYPE  61 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     46  142
  8P LOSS WILD-TYPE   61  159
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              46                61
  MALE               142               159
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   165   7
  8P LOSS WILD-TYPE 199  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    165    7
  8P LOSS WILD-TYPE  199   13
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              165               199
  YES               7                13
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, continuous
D56V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED      12                        12   158
  8P LOSS WILD-TYPE    31                        10   169
D56V12, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                  12                31
  BLACK OR AFRICAN AMERICAN              12                10
  WHITE                                 158               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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 204 163
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               38               367 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               163 
$`8Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-DK-A2HX TCGA-DK-A6B5 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SL 
      108.95        46.68        50.70         1.22         4.01        23.41 
TCGA-FD-A3SR TCGA-FJ-A3Z7 TCGA-GU-A42P TCGA-K4-A3WS TCGA-K4-A3WU TCGA-R3-A69X 
       19.79        31.07        10.92        25.02         3.45        14.24 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-AAMQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-5N-A9KI 
       34.45         4.21        71.57       104.65         8.35         2.50 
TCGA-BT-A42F TCGA-CF-A1HS TCGA-CF-A8HX TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA76 
       28.41        12.56        11.34        13.58         8.15        12.03 
TCGA-E7-A677 TCGA-E7-A6MD TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A6TK TCGA-G2-AA3F 
       26.96         4.24        19.33        27.45        10.85        29.36 
TCGA-GU-A762 TCGA-H4-A2HQ TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-UY-A78L TCGA-XF-AAN0 
        7.63        19.40        17.72        15.58        37.05        56.48 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

$`8Q LOSS WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 
       13.58         2.14        19.00        16.70       130.88        87.32 
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-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-AA6R TCGA-DK-AA6S 
       15.68        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
       25.58         0.92        33.04        60.66        24.30        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y 
       29.16        46.78        12.85        27.35         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P 
       12.36         3.06         4.31         9.67        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       24.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A4AC 
        8.58        19.07        22.72         9.01         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-S5-A6DX 
       27.68        52.73        50.56        35.97        46.98         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       33.14        86.83        51.32        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SW 
       15.35         3.22        15.98        14.93        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       13.74        10.82        11.31        54.90         7.63        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       24.13        11.97        94.88        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        47.80        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 
       17.16        16.18         4.67        17.56        36.43         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       23.01        12.79        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-A8HY TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       13.08         5.19        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        7.79       142.78         4.80        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC 
       15.02        13.58        18.81        19.00        15.35        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
        0.56         0.66        26.24        24.03        24.66        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62N 
       25.74        22.98        14.96        20.91         5.36         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        7.10        13.35         2.27        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.23        20.12        66.02         6.94        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.91        14.07         0.49         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       20.05        15.78         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.10         8.48        36.49         1.51        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
       12.16        21.24         9.07        11.70         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT 
       16.27        11.80        44.38         1.15        15.32        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       13.48        12.23        16.67        16.54        38.99        17.62 
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-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       35.24        29.56        17.82         6.21         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        6.58         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 
      110.60         2.96         8.32         6.77        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       18.84         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5N 
        5.52 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.22              0.49 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           108.95            166.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           18.525            17.620 
[1] "1.2 - 109.0 (18.5)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         0        8        12       18
  8Q LOSS WILD-TYPE       2      121       128      117
D57V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II                8               121
  STAGE III              12               128
  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
  8Q LOSS MUTATED          6  16  12
  8Q LOSS WILD-TYPE      117 179  46
D57V4, multiclass
          clus
vv         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1+T2               6               117
  T3                    16               179
  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   6  10   1
  8Q LOSS WILD-TYPE 218  41  65   7
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              18               218
  N1               6                41
  N2              10                65
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    16   2
  8Q LOSS WILD-TYPE 176   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     16    2
  8Q LOSS WILD-TYPE  176    9
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              16               176
  1               2                 9
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    13  25
  8Q LOSS WILD-TYPE  94 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     13   25
  8Q LOSS WILD-TYPE   94  276
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              13                94
  MALE                25               276
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    33   0
  8Q LOSS WILD-TYPE 331  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     33    0
  8Q LOSS WILD-TYPE  331   20
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               33               331
  YES               0                20
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, continuous
D57V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       3                         3    31
  8Q LOSS WILD-TYPE    40                        19   296
D57V12, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   3                40
  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  37
  8Q LOSS WILD-TYPE   9 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   37
  8Q LOSS WILD-TYPE    9  332
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 9
  NOT HISPANIC OR LATINO              37               332
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   100  72
  9P LOSS WILD-TYPE 127 106
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              172               233 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               72               106 
$`9P LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-CF-A9FL 
      108.95        16.27        26.14        14.89         8.35        18.58 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
        4.90        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 
        8.22        17.72        50.27        21.30        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       64.18        15.68        50.70       166.03        13.64        13.64 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SM 
       11.18        20.32        25.58         0.92         1.22        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y 
       29.16        46.78        19.79        12.85         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
       26.73        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3YS 
       12.69         3.06        11.08        17.62        21.40        24.92 
TCGA-GU-AATP TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       32.98        27.35        22.72        25.02         3.45         2.76 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HF 
       50.56        35.97        46.98        14.24         1.84        97.12 
TCGA-XF-A9SK TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       15.98        12.76        26.27        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       44.32        30.94        18.58        21.11        94.29         3.48 
TCGA-ZF-A9RL TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O 
       88.87        11.97        94.88       104.65         8.35        16.83 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-5N-A9KM TCGA-BT-A0S7 TCGA-BT-A20J 
       34.98        50.04         0.62        17.42         6.58        19.04 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.88        19.50        16.18        36.43        23.01        12.79 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47V 
       13.97        12.59        12.13        13.08        12.16        12.46 
TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A5W6 
       12.62        13.12        12.00        11.34        11.87         1.84 
TCGA-DK-A1A3 TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3WX TCGA-DK-AA6P 
       21.86        17.62        15.62         4.80        10.55        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       13.58        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A7PW TCGA-E7-A97Q 
       29.72         0.56         0.66         4.24        13.68         8.09 
TCGA-FD-A3B5 TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TK 
        8.94        22.98         5.36        27.45         7.10        10.85 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A4ZW 
       59.31         7.23        66.02        29.36        14.07         0.49 
TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATQ 
        8.94         2.20        11.31         7.63         4.73         7.00 
TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV 
       21.34         8.48        19.40        38.60        64.01        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        9.07        11.70        15.42        11.80        44.38         1.15 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A8OB 
       21.07        12.23        16.67        16.54        38.99        69.34 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HI TCGA-XF-A9SU TCGA-XF-A9T4 
      112.83        17.82         6.21        17.88         5.98        16.27 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R9 TCGA-ZF-AA4U TCGA-ZF-AA4W 
        6.77        11.97        25.41        28.41         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-GU-AATO 
       56.35        19.40         8.52        10.65 

$`9P LOSS WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A2LD TCGA-BT-A3PJ 
       16.77        15.12        33.83        12.39        20.48        25.94 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YR TCGA-DK-A1AC 
        9.96        28.70         8.98        12.92        15.12       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 
       46.68        87.32        23.21         9.67        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA74 
       67.36        36.66        38.24        52.01       165.73        56.15 
TCGA-E5-A4TZ TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       15.35        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A43P TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A6TC 
       27.35        53.88        10.78         5.69         8.25         6.15 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES 
       12.36         4.31         9.67        31.07        17.23        33.01 
TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ 
       70.32        19.13        17.75        10.92        32.78        19.82 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-K4-A54R 
       20.28         8.58        19.07         9.01         9.14        27.68 
TCGA-KQ-A41N TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
       52.73        33.14        86.83        51.32        97.45       125.49 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW 
       15.35         3.22        34.45        14.93         4.21        11.90 
TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       21.04        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAN2 TCGA-XF-AAN3 
       10.82        11.31        54.90         7.63        61.45        86.30 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-AA4R TCGA-ZF-AA4T 
        3.88         9.63        13.64        30.28        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7W 
       57.90        12.23        24.13        44.94        17.16        27.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20O 
       40.08         7.33         2.66         6.74        13.15        12.16 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH 
        5.06        14.96         5.06         8.25        17.16         4.67 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T 
       17.56        28.41         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-A3QU 
       12.10        12.26        12.10        11.34        13.08         5.19 
TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 
       29.79        66.41        18.41       112.44        16.14        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY 
        7.79       142.78        13.58         8.15        20.81       163.30 
TCGA-DK-AA6T TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 
       18.81         5.36        22.16         2.24        16.70        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       14.37        32.02        16.77        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N 
        5.52        25.74        14.96        20.91        19.33         2.70 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
       13.35         2.27        12.66        10.65         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-AA3C 
       61.94        48.00        15.95        26.93        20.12         6.94 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       20.71        15.81        15.91        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV 
        3.12        20.98        18.97        20.05        15.78        14.27 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A5RJ TCGA-K4-A6FZ 
       19.10        36.49         1.51        12.16        17.72         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A78L 
       16.27        15.32        15.58        13.48        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        76.01        78.25         3.02        35.24        29.56 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH 
        3.85        45.04         6.58         1.87        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAME TCGA-XF-AAMG 
       79.66        66.41        23.64        28.24        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
        2.96         8.32        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
        0.66        22.36        31.20        35.84        21.86        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V 
       64.08        58.72        47.84        20.22         2.89        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       67.20        35.41        54.21        29.49         5.52 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.49              0.66 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           166.03            165.73 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           16.605            18.840 
[1] "0.5 - 166.0 (16.6)" "0.7 - 165.7 (18.8)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         0       54        68       51
  9P LOSS WILD-TYPE       2       75        72       84
D58V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 0                 2
  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         52  87  25
  9P LOSS WILD-TYPE       71 108  33
D58V4, multiclass
          clus
vv         9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1+T2              52                71
  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 126  30  45   4
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             110               126
  N1              17                30
  N2              30                45
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    84   4
  9P LOSS WILD-TYPE 108   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     84    4
  9P LOSS WILD-TYPE  108    7
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              84               108
  1               4                 7
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    44 130
  9P LOSS WILD-TYPE  63 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     44  130
  9P LOSS WILD-TYPE   63  171
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              44                63
  MALE               130               171
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   156  10
  9P LOSS WILD-TYPE 208  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    156   10
  9P LOSS WILD-TYPE  208   10
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              156               208
  YES              10                10
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, continuous
D58V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED      19                         8   138
  9P LOSS WILD-TYPE    24                        14   189
D58V12, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                  19                24
  BLACK OR AFRICAN AMERICAN               8                14
  WHITE                                 138               189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     4 158
  9P LOSS WILD-TYPE   5 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  158
  9P LOSS WILD-TYPE    5  211
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO             158               211
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    99  69
  9Q LOSS WILD-TYPE 128 109
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              168               237 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               69               109 
$`9Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A42C 
      108.95        16.27        33.83        26.14        14.89        28.70 
TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       18.58         4.90        18.48        13.58         2.14        19.00 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 
       17.72        50.27        21.30        17.98        64.18        50.70 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU 
      166.03        13.64        11.18        20.32        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
        1.22        33.04        17.98        46.78        19.79        12.85 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
        3.62        15.58        26.73        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3BM 
       62.86        18.81         3.06        11.08        17.62        21.40 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU 
       32.78        32.98        19.07        22.72        25.02         3.45 
TCGA-K4-A4AB TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
        2.76        50.56        35.97        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-XF-A8HF TCGA-XF-A9SK TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-AAMQ 
       33.14        97.12        15.98        12.76        26.27        71.57 
TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 
       91.73        44.32        30.94        18.58        13.64        21.11 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       94.29         3.48        88.87        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
      104.65         8.35        16.83        34.98        50.04         0.62 
TCGA-4Z-AA83 TCGA-5N-A9KM TCGA-BT-A0S7 TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A2LB 
       66.54        17.42         6.58        17.88        19.50        16.18 
TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       36.43        23.01        12.79        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A8HX 
       13.08        10.95        12.46        12.62        13.12        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AD 
       11.34        11.87        13.08         5.19         1.84       112.44 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X 
       17.62        15.62        10.55        15.02        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A519 TCGA-E7-A5KE 
       12.03        43.59        38.83        29.72        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A43N 
        0.66         4.24        13.68         8.09         8.94        22.98 
TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       27.45         7.10         2.27        15.95        26.93        59.31 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 
       66.02        29.36        14.07         0.49         8.94        26.70 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10         2.20         4.73         7.00        14.27        21.34 
TCGA-GV-A3QH TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-AAQO 
        8.48        38.60        64.01        21.24        11.70        11.80 
TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78O 
        1.15        21.07        16.67        16.54        38.99        76.01 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HI TCGA-XF-A9SU TCGA-XF-A9T4 TCGA-XF-AAMW 
      112.83        17.82        17.88         5.98        16.27         8.32 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R9 
        6.77        11.97        22.36        25.41        31.20        28.41 
TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-GU-AATO 
       20.22         8.61        60.16        56.35        19.40        10.65 

$`9Q LOSS WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ 
       16.77        15.12        12.39         8.35        20.48        25.94 
TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YR TCGA-DK-A1AB TCGA-DK-A1AC 
        9.96         8.98        12.92        15.12        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
       46.68        87.32         8.22        23.21         9.67        66.05 
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-AA6R TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-FD-A3B7 
       52.01       165.73        13.64        56.15        15.35         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43P TCGA-FD-A5BS 
       60.66        24.30        23.41        29.16        27.35        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       10.78         5.69         8.25         6.15        12.69        12.36 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-AA3D 
        4.31         9.67        31.07        17.23        33.01        70.32 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3JZ TCGA-GV-A3QF 
       19.13        17.75        24.92        10.92        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       27.35         8.58         9.01         9.14        27.68        52.73 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SJ 
       86.83        51.32        97.45       125.49        15.35         3.22 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 
       34.45        14.93         4.21        11.90        21.04        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 
       54.90         7.63        98.99        61.45        86.30         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9R4 TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        9.63        30.28        34.06        19.69        57.90        12.23 
TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 
       44.94        17.16        27.62        41.75        51.16        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80         2.50        40.08         7.33         2.66         6.74 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       13.15        19.04        12.16         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 
        8.25        17.16         4.67        17.56        28.41         1.94 
TCGA-CF-A1HS TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA 
       12.56        12.16        12.66        12.10        12.26        12.00 
TCGA-CF-A7I0 TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE 
       12.10        29.79        21.86        66.41        18.41        16.14 
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-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       20.81       163.30        13.58        18.81         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        2.24        26.96        26.24        24.03        24.66        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 
       12.95        15.32        14.37        32.02        16.77        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U 
       22.52        27.98         5.52        25.74        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 
       19.33         5.36         2.70        13.35        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A3IB 
       10.65         8.94         3.25        61.94        48.00         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I3 
       20.12         6.94        20.71        15.81        15.91        13.91 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        3.12        20.98        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5NE 
       15.78        19.10        36.49         1.51        19.40        12.16 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R 
        9.07        17.72         1.81        15.42        16.27        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-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        78.25        69.34         3.02        35.24        29.56 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG 
        6.21         3.85        45.04         6.58         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAME 
       64.80        79.66        66.41        23.64        28.24        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
      110.60         2.96        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
        0.66        35.84        21.86        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 
       47.84         2.89        59.38        67.20        35.41         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       54.21        29.49         5.52 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.49              0.66 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           166.03            165.73 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            17.77             17.56 
[1] "0.5 - 166.0 (17.8)" "0.7 - 165.7 (17.6)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         1       57        61       49
  9Q LOSS WILD-TYPE       1       72        79       86
D59V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 1                 1
  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         55  79  24
  9Q LOSS WILD-TYPE       68 116  34
D59V4, multiclass
          clus
vv         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1+T2              55                68
  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 131  31  47   4
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             105               131
  N1              16                31
  N2              28                47
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    88   4
  9Q LOSS WILD-TYPE 104   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     88    4
  9Q LOSS WILD-TYPE  104    7
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              88               104
  1               4                 7
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    43 126
  9Q LOSS WILD-TYPE  64 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     43  126
  9Q LOSS WILD-TYPE   64  175
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              43                64
  MALE               126               175
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   151  10
  9Q LOSS WILD-TYPE 213  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    151   10
  9Q LOSS WILD-TYPE  213   10
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              151               213
  YES              10                10
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, continuous
D59V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED      20                         6   133
  9Q LOSS WILD-TYPE    23                        16   194
D59V12, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                  20                23
  BLACK OR AFRICAN AMERICAN               6                16
  WHITE                                 133               194
[1] 3 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     3 151
  9Q LOSS WILD-TYPE   6 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3  151
  9Q LOSS WILD-TYPE    6  218
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 6
  NOT HISPANIC OR LATINO             151               218
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    40  33
  10P LOSS WILD-TYPE 187 145
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                73                332 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                33                145 
$`10P LOSS MUTATED`
TCGA-BT-A2LD TCGA-BT-A42C TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A3IS 
       20.48        28.70         4.90        15.12        18.48        50.27 
TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A4TZ 
       67.36        38.24        52.01        13.64        11.18        15.35 
TCGA-E7-A541 TCGA-FD-A3B7 TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A6TD 
       25.58         4.01        19.79        15.58         8.25        12.69 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GV-A40G TCGA-K4-A3WU TCGA-KQ-A41O 
       31.07        17.23        21.40        19.07         3.45        50.56 
TCGA-XF-A8HE TCGA-XF-A9SV TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-ZF-A9RE TCGA-2F-A9KP 
      125.49        12.76        10.82        54.90         3.48        11.97 
TCGA-2F-A9KR TCGA-4Z-AA82 TCGA-BT-A20U TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-C4-A0F6 
      104.65        51.16        14.96        17.16         1.94        23.01 
TCGA-CF-A27C TCGA-CF-A8HY TCGA-DK-A2I2 TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       13.97        11.34         7.79        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A43N TCGA-FJ-A3ZE 
       43.59        16.77         8.94        22.52        22.98        10.65 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GV-A3JX TCGA-GV-A3QI 
       26.93         7.23        15.91        13.91        19.10        36.49 
TCGA-H4-A2HQ TCGA-K4-A5RH TCGA-K4-A5RI TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       19.40         9.07        11.70        15.58        13.48        12.23 
TCGA-UY-A78O TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI 
       76.01        29.56         6.21         1.87        48.62        79.66 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9RD TCGA-ZF-AA4N TCGA-ZF-AA4W 
        6.77        11.97        25.41        13.41         2.89        60.16 
TCGA-ZF-AA4X 
       67.20 

$`10P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ 
       26.14        14.89         8.35        25.94         9.96         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       18.58        12.92        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
      130.88        46.68        87.32         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA6S 
       76.60        15.68        50.70        36.66       165.73       166.03 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       13.64        56.15        20.32         0.92         1.22        33.04 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       60.66        24.30        23.41        17.98        29.16        46.78 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        5.69        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FT-A61P 
        6.15        12.36         3.06         4.31         9.67        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       33.01        17.62        70.32        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC 
        8.58        22.72         9.01        25.02         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       27.68        52.73        35.97        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       33.14        86.83        51.32        97.45        97.12        15.35 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW 
        3.22        15.98        34.45        14.93         4.21        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       13.74        11.31         7.63        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       44.32        30.94        61.45        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL 
        9.63        13.64        21.11        30.28        94.29        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KQ 
       34.06        19.69        57.90        12.23        24.13        94.88 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        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-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-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-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         5.06         8.25        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG 
       36.43        28.41        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
       17.95       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-E5-A4U1 
       10.55       163.30        15.02        13.58        18.81        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         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-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-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S 
       32.02        12.62        27.98         5.52        25.74        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE 
       13.35         2.27        10.85        12.66         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B 
       61.94        48.00        15.95        59.31        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW 
        6.94        29.36        20.71        15.81        14.07         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HO TCGA-HQ-A2OE 
        7.00        14.27        21.34         8.48         1.51        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       64.01        12.16        21.24        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT 
       16.27        11.80        44.38         1.15        15.32        21.07 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD 
       78.25        69.34         3.02       112.83        35.24        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL 
        3.85        45.04         6.58        17.88        64.80        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
        2.96         8.32        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        0.66        22.36        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V 
       64.08        58.72        47.84        20.22         8.61        59.38 
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        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.87               0.49 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            125.49             166.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            15.910             17.785 
[1] "1.9 - 125.5 (15.9)" "0.5 - 166.0 (17.8)"
[1] "hr=" "1.1"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         0       26        25       22
  10P LOSS WILD-TYPE       2      103       115      113
D60V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                26                103
  STAGE III               25                115
  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
  10P LOSS MUTATED         22  31   8
  10P LOSS WILD-TYPE      101 164  50
D60V4, multiclass
          clus
vv         10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1+T2               22                101
  T3                     31                164
  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
  10P LOSS MUTATED    46   8  11   2
  10P LOSS WILD-TYPE 190  39  64   6
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               46                190
  N1                8                 39
  N2               11                 64
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    31   3
  10P LOSS WILD-TYPE 161   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     31    3
  10P LOSS WILD-TYPE  161    8
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               31                161
  1                3                  8
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    20  53
  10P LOSS WILD-TYPE  87 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20   53
  10P LOSS WILD-TYPE   87  248
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               20                 87
  MALE                 53                248
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    65   6
  10P LOSS WILD-TYPE 299  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     65    6
  10P LOSS WILD-TYPE  299   14
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                65                299
  YES                6                 14
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, continuous
D60V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       4                         9    54
  10P LOSS WILD-TYPE    39                        13   273
D60V12, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                9                 13
  WHITE                                   54                273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  66
  10P LOSS WILD-TYPE   7 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   66
  10P LOSS WILD-TYPE    7  303
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               66                303
[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 158 119
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               128                277 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                59                119 
$`10Q LOSS MUTATED`
TCGA-4Z-AA7Q TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C TCGA-CU-A0YO 
       16.77        26.14         8.35        20.48        28.70         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IS 
       15.12        18.48         2.14        46.68        87.32        50.27 
TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       66.05        67.36        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV 
      166.03        13.64        11.18        15.35        25.58         1.22 
TCGA-FD-A3B7 TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A5C1 
        4.01        19.79        27.35        15.58         8.25        58.92 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY 
       12.69        12.36        31.07        17.23        11.08        17.62 
TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GU-A42P TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA 
       21.40        17.75        10.92        20.28        19.07        22.72 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-KQ-A41O TCGA-KQ-A41P TCGA-XF-A8HF 
       25.02         3.45         9.14        50.56        35.97        97.12 
TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
        3.22        14.93        12.76        10.82        54.90         7.63 
TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-2F-A9KP 
       18.58        13.64        21.11         3.48        19.69        11.97 
TCGA-2F-A9KR TCGA-4Z-AA7R TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20U 
      104.65        17.16         2.50        40.08         2.66        14.96 
TCGA-BT-A2LA TCGA-BT-A42B TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A8HY 
       17.16        17.56         1.94        23.01        13.97        11.34 
TCGA-CU-A3QU TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6P 
        5.19         7.79         4.80        13.58         8.15        15.02 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ 
       19.00        15.35        12.03        43.59        29.72        22.16 
TCGA-E7-A6ME TCGA-FD-A3N5 TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A6TF TCGA-FJ-A3ZE 
       24.03        22.52        22.98        20.91         2.27        10.65 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 
        7.23        20.12        15.91        14.07         0.49        13.91 
TCGA-GD-A3OP TCGA-GU-A764 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        2.10        20.05        21.34        19.10         8.48        36.49 
TCGA-H4-A2HQ TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41S TCGA-LT-A5Z6 
       19.40         9.07        11.70         1.81         1.15        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD 
       13.48        12.23        76.01        69.34        35.24        17.82 
TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-AAMW 
        6.21         6.58         1.87        48.62        79.66         8.32 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X 
        6.77        11.97        22.36         2.89         8.61        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 
       56.35        35.41 

$`10Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T 
      108.95        16.27        15.12        33.83        12.39        14.89 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A72E 
       25.94         9.96         8.98        18.58        12.92        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
       19.00        16.70       130.88         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21         9.67        17.98        64.18        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A7DU 
       15.68        50.70        13.64        56.15        20.32         0.92 
TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       33.04        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       46.78        12.85         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        5.69        18.08         6.28        62.86        18.81         6.15 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB 
        3.06         4.31         9.67        33.01        70.32        19.13 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E 
       24.92        32.78        32.98        19.82        27.35         8.58 
TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X 
        9.01         2.76        27.68        52.73        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
        1.84        33.14        86.83        51.32        97.45       125.49 
TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY 
       15.35        15.98        34.45         4.21        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       11.31        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       61.45        86.30         3.88         9.63        30.28        94.29 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KQ 
       88.87        34.06        57.90        12.23        24.13        94.88 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
        8.35        44.94        16.83        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       17.42         7.33         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X 
       12.16        17.88        19.50         5.06         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS 
       16.18         4.67        36.43        28.41        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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.34        11.87        13.08        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       15.62        17.95       142.78        20.81        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       13.58        18.81        38.83         5.36         2.24        16.70 
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-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-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO 
       32.02        16.77         8.94        12.62        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       25.74        14.96        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE 
        7.10        13.35        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-AA3B 
       61.94        48.00        15.95        26.93        59.31        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GD-A2C5 
        6.94        29.36        20.71        15.81         8.94        26.70 
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-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-H4-A2HO TCGA-HQ-A2OE 
       15.78         4.73         7.00        14.27         1.51        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
       64.01        12.16        21.24        17.72        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 
       11.80        44.38        15.32        21.07        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OC 
       38.99        17.62        37.05        22.68        78.25         3.02 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HI TCGA-XF-A9SH 
      112.83        29.56         3.85        45.04        17.88        64.80 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
      110.60         2.96        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        0.66        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4V 
       13.41        64.08        58.72        47.84        20.22        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       60.16        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.49               0.56 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            166.03             163.30 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            16.965             17.950 
[1] "0.5 - 166.0 (17.0)" "0.6 - 163.3 (17.9)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         1       45        41       42
  10Q LOSS WILD-TYPE       1       84        99       93
D61V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                45                 84
  STAGE III               41                 99
  STAGE IV                42                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  10Q LOSS MUTATED         39  57  17
  10Q LOSS WILD-TYPE       84 138  41
D61V4, multiclass
          clus
vv         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1+T2               39                 84
  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
  10Q LOSS MUTATED    67  12  23   4
  10Q LOSS WILD-TYPE 169  35  52   4
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               67                169
  N1               12                 35
  N2               23                 52
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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  96
  10Q LOSS WILD-TYPE  74 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     33   96
  10Q LOSS WILD-TYPE   74  205
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               33                 74
  MALE                 96                205
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   111   9
  10Q LOSS WILD-TYPE 253  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    111    9
  10Q LOSS WILD-TYPE  253   11
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO               111                253
  YES                9                 11
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, continuous
D61V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       8                         8   105
  10Q LOSS WILD-TYPE    35                        14   222
D61V12, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    8                 35
  BLACK OR AFRICAN AMERICAN                8                 14
  WHITE                                  105                222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4 117
  10Q LOSS WILD-TYPE   5 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  117
  10Q LOSS WILD-TYPE    5  252
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO              117                252
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    95  81
  11P LOSS WILD-TYPE 132  97
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               176                229 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                81                 97 
$`11P LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
      108.95        15.12        33.83        26.14        14.89         8.35 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AB 
       28.70         8.98        18.48        13.58         2.14        16.70 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 
       46.68        87.32        17.72        50.27        21.30        17.98 
TCGA-DK-A6AV TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 
       64.18        38.24       166.03        13.64        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
       15.35        25.58         0.92        24.30        23.41        29.16 
TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA 
       12.85        15.58        26.73        18.08        58.92        62.86 
TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES 
        6.15         3.06         4.31        31.07        11.08        33.01 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A40G 
       70.32        21.40        24.92        32.98        20.28        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X 
       22.72         9.01        52.73        50.56        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9ST 
        1.84        33.14        15.35         3.22        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAML 
       12.76        11.90        66.64         2.10        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       71.57        91.73        44.32        18.58        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-2F-A9KR 
       94.29        88.87        34.06        19.69        24.13       104.65 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       16.83        34.98         0.62         2.50        17.42        40.08 
TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0F6 TCGA-CF-A1HR 
        5.06        17.16         4.67        17.56        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-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FF 
       12.62        13.12        12.00        12.10        11.34        11.87 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.84        66.41       112.44        17.95         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
        8.15        15.02        19.00        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW 
       29.72        22.16         0.56         4.24        24.03        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A43N TCGA-FD-A5BZ 
       12.95        14.37         8.09         8.94        22.98        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-G2-A2EO TCGA-G2-AA3B 
        2.70         7.10         2.27        10.65        59.31        66.02 
TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       29.36        14.07         2.10         2.20        11.31        18.97 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-H4-A2HQ TCGA-HQ-A2OE 
        4.73         7.00        14.27        21.34        19.40        38.60 
TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
       64.01        11.70        15.42        11.80        44.38         1.15 
TCGA-LT-A8JT TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       21.07        16.54        38.99        22.68        76.01        69.34 
TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SU 
        3.02        17.82         6.21        48.62        64.80         5.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
      110.60         2.96         8.32         6.77        56.48        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U 
       22.36        25.41        13.41        47.84        20.22         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA5H 
       67.20        29.49 

$`11P LOSS WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-BL-A5ZZ TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       16.27        16.77        12.39        20.48        25.94         9.96 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1AA TCGA-DK-A1AC 
       18.58        12.92         4.90        15.12        19.00       130.88 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
        8.22        23.21         9.67        66.05        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R 
       67.36        15.68        50.70        36.66        52.01       165.73 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       13.64        56.15         1.22        33.04         4.01        60.66 
TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS 
       17.98        46.78        19.79        27.35         3.62        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD 
       10.78         5.69         8.25         6.28        18.81        12.69 
TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3WC 
       12.36         9.67        17.23        17.62        19.13        17.75 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-K4-A3WS 
       10.92        32.78        19.82        27.35         8.58        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41P TCGA-UY-A78N 
        3.45         2.76         9.14        27.68        35.97        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SK TCGA-XF-A9SM 
       51.32        97.45       125.49        97.12        15.98        34.45 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T8 TCGA-XF-AAMF 
       21.04        26.27        18.90         2.24        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 
       11.31        98.99        30.94        61.45        86.30         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9RE TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP 
        9.63        13.64         3.48        57.90        12.23        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       94.88         8.35        44.94        17.16        27.62        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13I 
       41.75        51.16        66.54        10.22        47.80         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         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-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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.10        12.26        11.34        13.08         5.19        29.79 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       21.86        18.41        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
      142.78        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6X TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       15.35         5.36         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 
       26.24        24.66        14.07        15.32        32.02        16.77 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S 
       12.62        22.52        27.98         5.52        25.74        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 
       20.91        19.33         5.36        13.35        10.85        12.66 
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-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
        7.23        20.12         6.94        20.71        15.81        15.91 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS 
        0.49         8.94        13.91        26.70         3.12        20.98 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.63        20.05        15.78        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
        1.51        12.16        21.24         9.07        17.72         1.81 
TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       16.27        15.32        15.58        13.48        12.23        16.67 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       17.62        37.05        78.25       112.83        35.24        29.56 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI 
        3.85        45.04         6.58         1.87        17.88        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAN4 
       66.41        23.64        28.24        16.27        92.98        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       75.39        18.84         0.66        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W 
       28.41        64.08        58.72         2.89        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       56.35        35.41        19.40         8.52        54.21         5.52 
TCGA-GU-AATO 
       10.65 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.56               0.49 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            166.03             165.73 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             17.77              17.62 
[1] "0.6 - 166.0 (17.8)" "0.5 - 165.7 (17.6)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         1       52        54       70
  11P LOSS WILD-TYPE       1       77        86       65
D62V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                52                 77
  STAGE III               54                 86
  STAGE IV                70                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  11P LOSS MUTATED         57  87  27
  11P LOSS WILD-TYPE       66 108  31
D62V4, multiclass
          clus
vv         11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1+T2               57                 66
  T3                     87                108
  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
  11P LOSS MUTATED    94  25  40   3
  11P LOSS WILD-TYPE 142  22  35   5
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               94                142
  N1               25                 22
  N2               40                 35
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    89   7
  11P LOSS WILD-TYPE 103   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     89    7
  11P LOSS WILD-TYPE  103    4
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               89                103
  1                7                  4
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    46 132
  11P LOSS WILD-TYPE  61 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     46  132
  11P LOSS WILD-TYPE   61  169
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               46                 61
  MALE                132                169
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   156  10
  11P LOSS WILD-TYPE 208  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    156   10
  11P LOSS WILD-TYPE  208   10
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO               156                208
  YES               10                 10
[1] 2 2
[1] FALSE
D62V9, continuous
D62V10, continuous
D62V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED      25                         8   134
  11P LOSS WILD-TYPE    18                        14   193
D62V12, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                   25                 18
  BLACK OR AFRICAN AMERICAN                8                 14
  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"
D62V13, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5 157
  11P LOSS WILD-TYPE   4 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5  157
  11P LOSS WILD-TYPE    4  212
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO              157                212
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    69  59
  11Q LOSS WILD-TYPE 158 119
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               128                277 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                59                119 
$`11Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A42C 
      108.95        33.83        26.14        14.89         8.35        28.70 
TCGA-C4-A0EZ TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IN 
        8.98        18.48         2.14        16.70        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-DK-AA6W 
       17.72        50.27        64.18        36.66       166.03        13.64 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3SJ TCGA-FD-A43Y 
       11.18        15.35        25.58         0.92        24.30        15.58 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FT-A61P 
        8.25        18.08        58.92         6.15         4.31        11.08 
TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GV-A3QK TCGA-GV-A40G TCGA-HQ-A5ND 
       33.01        21.40        24.92        27.35        19.07         9.01 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-XF-A8HG TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV 
       50.56        46.98        15.35        34.45        14.93        12.76 
TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       11.90        66.64         2.10        54.90         7.63        71.57 
TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4R 
       61.45        18.58        21.11        30.28        94.29        34.06 
TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-5N-A9KI 
       19.69        24.13       104.65        16.83        34.98         2.50 
TCGA-BL-A0C8 TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-CF-A1HS 
       40.08         5.06        17.16         4.67        17.56        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A5U8 
       13.97        12.59        12.13        12.16        12.62        13.12 
TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I1 
       12.10        11.34         1.84        66.41       112.44        17.95 
TCGA-DK-A3IL TCGA-DK-AA6P TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD 
       13.58        15.02        43.59        22.16         0.56         4.24 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 
       24.03        13.68        12.95        14.37         8.09         8.94 
TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O TCGA-G2-A2EO TCGA-GC-A6I1 
       22.98         5.36         2.70         7.10        59.31         8.94 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10         2.20        11.31         7.00        14.27        21.34 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-KQ-A41R TCGA-KQ-A41S 
       19.40        38.60        64.01        11.70        44.38         1.15 
TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE 
       38.99        76.01        69.34       112.83        29.56         6.21 
TCGA-XF-A9SG TCGA-XF-A9SU TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       48.62         5.98       110.60         2.96         8.32        56.48 
TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA54 
       22.36        13.41        20.22         8.61        67.20        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5H 
       54.21        29.49 

$`11Q LOSS WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A2LD TCGA-BT-A3PJ 
       16.27        16.77        15.12        12.39        20.48        25.94 
TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E 
        9.96        18.58        12.92         4.90        15.12        13.58 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       19.00       130.88        46.68        21.30        23.21         9.67 
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-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA71 TCGA-DK-AA74 
       50.70        38.24        52.01       165.73        13.64        56.15 
TCGA-DK-AA77 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL 
       20.32         1.22        33.04         4.01        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A62P 
        3.62        26.73        53.88        10.78         5.69         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI 
       62.86        18.81        12.69        12.36         3.06         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
       31.07        17.23        17.62        70.32        19.13        17.75 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E 
       10.92        32.78        32.98        19.82        20.28         8.58 
TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       22.72        25.02         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       52.73        35.97        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SK 
       51.32        97.45       125.49        97.12         3.22        15.98 
TCGA-XF-A9ST TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T8 
        4.21        21.04        26.27        18.90         2.24        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       10.82        11.31        91.73        98.99        44.32        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9RE TCGA-ZF-A9RL 
       86.30         3.88         9.63        13.64         3.48        88.87 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N 
       57.90        12.23        11.97        94.88         8.35        44.94 
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-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J 
       66.54        10.22        47.80        17.42         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-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A42E 
       19.50         5.06        14.96         8.25        16.18        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MH TCGA-CF-A47S 
       28.41         1.94        23.01        12.79        13.08        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A8HX 
       12.66        12.46        12.10        12.26        12.00        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 
       11.87        13.08         5.19        29.79        21.86        18.41 
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-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
        8.15        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        12.03        38.83        29.72         5.36 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        2.24        16.70         0.66        26.96        26.24        24.66 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.07        15.32        32.02        16.77        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
       27.98         5.52        25.74        14.96        20.91        19.33 
TCGA-FD-A5BZ TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       27.45        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         0.49        13.91        26.70 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        3.12        20.98        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE 
        4.73        19.10         8.48        36.49         1.51        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       21.24         9.07        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        15.32        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P 
       16.67        16.54        17.62        37.05        22.68        78.25 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
        3.02        35.24        17.82         3.85        45.04         6.58 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        66.41        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 
       28.24        16.27        92.98         6.77        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       18.84         0.66        11.97        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N 
       21.86        28.41        64.08        58.72        47.84         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       59.38        60.16        56.35        35.41         8.52         5.52 
TCGA-GU-AATO 
       10.65 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.56               0.49 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            166.03             165.73 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             17.64              17.62 
[1] "0.6 - 166.0 (17.6)" "0.5 - 165.7 (17.6)"
[1] "hr=" "1"  
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         1       38        45       44
  11Q LOSS WILD-TYPE       1       91        95       91
D63V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                38                 91
  STAGE III               45                 95
  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
  11Q LOSS MUTATED         43  61  21
  11Q LOSS WILD-TYPE       80 134  37
D63V4, multiclass
          clus
vv         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1+T2               43                 80
  T3                     61                134
  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
  11Q LOSS MUTATED    71  18  23   1
  11Q LOSS WILD-TYPE 165  29  52   7
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               71                165
  N1               18                 29
  N2               23                 52
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    63   3
  11Q LOSS WILD-TYPE 129   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     63    3
  11Q LOSS WILD-TYPE  129    8
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               63                129
  1                3                  8
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    38  91
  11Q LOSS WILD-TYPE  69 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     38   91
  11Q LOSS WILD-TYPE   69  210
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               38                 69
  MALE                 91                210
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   113   9
  11Q LOSS WILD-TYPE 251  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    113    9
  11Q LOSS WILD-TYPE  251   11
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               113                251
  YES                9                 11
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, continuous
D63V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED      18                         6    97
  11Q LOSS WILD-TYPE    25                        16   230
D63V12, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                   18                 25
  BLACK OR AFRICAN AMERICAN                6                 16
  WHITE                                   97                230
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3 113
  11Q LOSS WILD-TYPE   6 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3  113
  11Q LOSS WILD-TYPE    6  256
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO              113                256
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    26  27
  12P LOSS WILD-TYPE 201 151
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                53                352 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                27                151 
$`12P LOSS MUTATED`
TCGA-DK-A1AC TCGA-DK-A3IV TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43X 
      130.88         9.67        23.41        46.78        19.79         3.62 
TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-FD-A6TH TCGA-G2-AA3D TCGA-GC-A3YS TCGA-SY-A9G0 
       18.08        12.36         4.31        70.32        24.92        33.14 
TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9T3 
       51.32        97.12        15.35         3.22        14.93         2.24 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-ZF-AA4T TCGA-2F-A9KW TCGA-5N-A9KI TCGA-BT-A2LA 
       10.82        54.90        19.69         8.35         2.50        17.16 
TCGA-C4-A0F0 TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-E5-A2PC 
        1.94        12.16        12.62         5.19         1.84        43.59 
TCGA-E7-A97Q TCGA-FD-A43N TCGA-G2-AA3F TCGA-GV-A3JW TCGA-KQ-A41R TCGA-KQ-A41S 
        8.09        22.98        29.36        21.34        44.38         1.15 
TCGA-LC-A66R TCGA-PQ-A6FN TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HH 
       15.32        16.67        22.68       112.83        17.82         1.87 
TCGA-XF-A9SH TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9R0 
       64.80       110.60         8.32        56.48        11.97        22.36 
TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA52 
       64.08        20.22         8.61        60.16        35.41 

$`12P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       28.70         8.98        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX 
       18.48        13.58         2.14        19.00        16.70        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
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-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       15.68        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      166.03        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.35        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43P 
       60.66        24.30        17.98        29.16        12.85        27.35 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        3.06         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 
       17.62        21.40        19.13        17.75        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X 
       27.68        52.73        50.56        35.97        46.98        14.24 
TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SK TCGA-XF-A9SM 
        1.84        86.83        97.45       125.49        15.98        34.45 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ 
       66.64         2.10        13.74        11.31         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P 
       94.29         3.48        88.87        34.06        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O 
       24.13        11.97        94.88       104.65        44.94        16.83 
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-5N-A9KM TCGA-BL-A0C8 
       51.16        66.54        10.22        47.80        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74         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-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        8.25        16.18         4.67        17.56        36.43        28.41 
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-A9FM TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       13.08        29.79        21.86        66.41        18.41       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-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
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-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-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
        5.52        25.74        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW 
        6.94        20.71        15.81        15.91        14.07         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        4.73         7.00        14.27        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
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-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-AA26 
       11.80        15.58        21.07        13.48        12.23        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       38.99        17.62        37.05        76.01        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
        3.02        35.24        29.56         6.21         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
        6.58        17.88        48.62        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMX 
       23.64        28.24        16.27        92.98         2.96         6.77 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       27.06        75.39        18.84         0.66        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM 
       35.84        21.86        28.41        13.41        58.72        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
        2.89        59.38        67.20        56.35        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1.15               0.49 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            130.88             166.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             18.08              17.62 
[1] "1.1 - 130.9 (18.1)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         0       13        19       22
  12P LOSS WILD-TYPE       2      116       121      113
D64V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                13                116
  STAGE III               19                121
  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
  12P LOSS MUTATED         16  24  13
  12P LOSS WILD-TYPE      107 171  45
D64V4, multiclass
          clus
vv         12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1+T2               16                107
  T3                     24                171
  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
  12P LOSS MUTATED    24   5  15   1
  12P LOSS WILD-TYPE 212  42  60   7
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               24                212
  N1                5                 42
  N2               15                 60
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    19   1
  12P LOSS WILD-TYPE 173  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     19    1
  12P LOSS WILD-TYPE  173   10
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               19                173
  1                1                 10
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    16  38
  12P LOSS WILD-TYPE  91 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     16   38
  12P LOSS WILD-TYPE   91  263
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               16                 91
  MALE                 38                263
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    47   3
  12P LOSS WILD-TYPE 317  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     47    3
  12P LOSS WILD-TYPE  317   17
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                47                317
  YES                3                 17
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, continuous
D64V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       5                         1    46
  12P LOSS WILD-TYPE    38                        21   281
D64V12, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                1                 21
  WHITE                                   46                281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2  49
  12P LOSS WILD-TYPE   7 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   49
  12P LOSS WILD-TYPE    7  320
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               49                320
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    31  26
  12Q LOSS WILD-TYPE 196 152
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                57                348 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                26                152 
$`12Q LOSS MUTATED`
TCGA-BT-A2LD TCGA-DK-A2I6 TCGA-DK-A3IV TCGA-DK-AA6R TCGA-FD-A3SL TCGA-FD-A3SQ 
       20.48        87.32         9.67       165.73        23.41        46.78 
TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-AA3D 
       12.85         3.62        12.36         4.31        11.08        70.32 
TCGA-GC-A3YS TCGA-K4-A4AC TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HG 
       24.92         9.14        33.14        51.32        97.12        15.35 
TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-4Z-AA86 
        3.22        14.93         2.24        10.82        54.90        10.22 
TCGA-5N-A9KI TCGA-C4-A0F0 TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A3QU TCGA-E5-A2PC 
        2.50         1.94        12.16        12.62         5.19        43.59 
TCGA-E7-A97Q TCGA-FD-A3SO TCGA-FD-A43N TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A4ZW 
        8.09         5.52        22.98        29.36        14.07         0.49 
TCGA-GV-A3JW TCGA-HQ-A5NE TCGA-K4-A5RJ TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       21.34        12.16        17.72        44.38         1.15        15.32 
TCGA-PQ-A6FN TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A9SH TCGA-XF-AAMG 
       16.67        22.68       112.83        17.82        64.80       110.60 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-ZF-A9R0 TCGA-ZF-A9RF TCGA-ZF-AA4U TCGA-ZF-AA4W 
        8.32        56.48        22.36        64.08         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
       67.20        35.41        29.49 

$`12Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       26.14        14.89         8.35        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 
        8.22        17.72        50.27        21.30        23.21        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-AA6S TCGA-DK-AA6W 
       50.70        36.66        38.24        52.01       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        56.15        11.18        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR 
       17.98        29.16        19.79        27.35        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG 
        6.28        62.86        18.81         6.15        12.69         3.06 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM 
        9.67        31.07        17.23        33.01        17.62        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       19.13        17.75        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
       25.02         3.45         2.76        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A8HD 
       35.97        46.98        14.24         1.84        86.83        97.45 
TCGA-XF-A8HE TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
      125.49        15.98        34.45         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       21.04        26.27        18.90        66.64         2.10        13.74 
TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       11.31         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
       13.64        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       66.54        47.80        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-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
       16.18         4.67        17.56        36.43        28.41        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-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       29.79         1.84        21.86        66.41        18.41       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-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
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-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-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       25.74        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        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-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       26.93        59.31         7.23        20.12        66.02         6.94 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       20.71        15.81        15.91         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
       64.01        21.24         9.07        11.70         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       16.27        11.80        15.58        21.07        13.48        12.23 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P 
       16.54        38.99        17.62        37.05        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        35.24        29.56         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI 
       45.04         6.58         1.87        17.88        48.62        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        2.96         6.77        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       11.97        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V 
       13.41        58.72        47.84        20.22         2.89        59.38 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       56.35        19.40         8.52        54.21         5.52        10.65 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.49               0.56 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            165.73             166.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             17.72              17.62 
[1] "0.5 - 165.7 (17.7)" "0.6 - 166.0 (17.6)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED         0       15        17       26
  12Q LOSS WILD-TYPE       2      114       123      109
D65V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                15                114
  STAGE III               17                123
  STAGE IV                26                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  12Q LOSS MUTATED         19  26  12
  12Q LOSS WILD-TYPE      104 169  46
D65V4, multiclass
          clus
vv         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1+T2               19                104
  T3                     26                169
  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
  12Q LOSS MUTATED    24  10  13   2
  12Q LOSS WILD-TYPE 212  37  62   6
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               24                212
  N1               10                 37
  N2               13                 62
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    23   1
  12Q LOSS WILD-TYPE 169  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     23    1
  12Q LOSS WILD-TYPE  169   10
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               23                169
  1                1                 10
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    15  43
  12Q LOSS WILD-TYPE  92 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     15   43
  12Q LOSS WILD-TYPE   92  258
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               15                 92
  MALE                 43                258
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    48   5
  12Q LOSS WILD-TYPE 316  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     48    5
  12Q LOSS WILD-TYPE  316   15
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                48                316
  YES                5                 15
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, continuous
D65V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       5                         2    49
  12Q LOSS WILD-TYPE    38                        20   278
D65V12, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    5                 38
  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"
D65V13, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  53
  12Q LOSS WILD-TYPE   8 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   53
  12Q LOSS WILD-TYPE    8  316
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  8
  NOT HISPANIC OR LATINO               53                316
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    45  40
  13Q LOSS WILD-TYPE 182 138
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                85                320 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                40                138 
$`13Q LOSS MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A42C TCGA-DK-A1A5 
       16.77        15.12        26.14        14.89        28.70         2.14 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A6B6 TCGA-DK-AA6W TCGA-DK-AA75 
      130.88        87.32         8.22        36.66        13.64        11.18 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A43P TCGA-FD-A5C1 
        1.22         4.01        24.30        29.16        27.35        58.92 
TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3YS TCGA-HQ-A5ND TCGA-K4-A4AC 
       17.23        33.01        21.40        24.92         9.01         9.14 
TCGA-KQ-A41Q TCGA-UY-A78N TCGA-XF-A9SM TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAMJ 
       46.98        86.83        34.45        21.04        66.64        54.90 
TCGA-XF-AAMZ TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-AA53 TCGA-4Z-AA7R TCGA-4Z-AA7W 
       44.32        21.11         3.48        57.90        17.16        27.62 
TCGA-4Z-AA82 TCGA-BL-A13J TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH 
       51.16         2.66         5.06         8.25        17.16         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A2I2 
       17.56        36.43         1.94         1.84        21.86         7.79 
TCGA-DK-A3IM TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A85H 
        8.15        29.72        22.16         0.56         4.24        12.95 
TCGA-FD-A3B5 TCGA-FD-A5BV TCGA-FD-A62N TCGA-G2-A2EO TCGA-G2-AA3F TCGA-GC-A6I1 
        8.94         5.36         2.70        59.31        29.36         8.94 
TCGA-GC-A6I3 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GV-A3JW TCGA-GV-A3QI TCGA-HQ-A2OE 
       13.91         2.20        11.31        21.34        36.49        38.60 
TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-KQ-A41S TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PD 
       21.24         1.81         1.15        69.34        29.56        17.82 
TCGA-UY-A9PF TCGA-XF-AAMG TCGA-XF-AAMX TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG 
        3.85       110.60         6.77        28.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 
       47.84        20.22         2.89        60.16        56.35        19.40 
TCGA-ZF-AA58 
       54.21 

$`13Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20W TCGA-BT-A2LD 
      108.95        16.27        33.83        12.39         8.35        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       25.94         9.96         8.98        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX 
       15.12        18.48        13.58        19.00        16.70        46.68 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
       17.72        50.27        21.30        23.21         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA71 
       50.70        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 
       56.15        20.32        15.35        25.58         0.92        33.04 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       60.66        23.41        17.98        46.78        19.79        12.85 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
        3.62        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        8.25        18.08         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 
       12.69        12.36         3.06         4.31         9.67        31.07 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P 
       11.08        17.62        70.32        19.13        17.75        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R 
       19.07        22.72        25.02         3.45         2.76        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       52.73        50.56        35.97        14.24         1.84        33.14 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       51.32        97.45       125.49        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 
       15.98        14.93         4.21        12.76        11.90        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90         2.24         2.10        13.74        10.82        11.31 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
        7.63        71.57        91.73        98.99        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 
       86.30        18.58         3.88         9.63        13.64        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KO 
       94.29        88.87        34.06        19.69        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 
       34.98        50.04         0.62        41.75        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       47.80         2.50        17.42        40.08         7.33         6.74 
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-A20U TCGA-BT-A2LB TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
        5.06        14.96        16.18        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       13.08         5.19        29.79        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK 
       16.14        17.62        15.62        17.95       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
       13.58        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       18.81        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        5.36         2.24        16.70         0.66        26.96        26.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.09        32.02        16.77        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
       27.45         7.10        13.35         2.27        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-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 
       26.93         7.23        20.12        66.02         6.94        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.81        15.91        14.07         0.49        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        3.12        20.98        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HO 
        4.73         7.00        14.27        19.10         8.48         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       19.40        64.01        12.16         9.07        11.70        17.72 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 
       15.42        16.27        11.80        44.38        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       21.07        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       17.62        37.05        22.68        76.01        78.25         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
      112.83        35.24         6.21        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW 
       23.64        28.24        16.27        92.98         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
       22.36        25.41        31.20        35.84        21.86        13.41 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H 
        8.61        59.38        67.20        35.41         8.52        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.56               0.49 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            130.88             166.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            21.040             17.125 
[1] "0.6 - 130.9 (21.0)" "0.5 - 166.0 (17.1)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         0       23        33       28
  13Q LOSS WILD-TYPE       2      106       107      107
D66V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  0                  2
  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         24  46  10
  13Q LOSS WILD-TYPE       99 149  48
D66V4, multiclass
          clus
vv         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1+T2               24                 99
  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 192  34  62   6
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               44                192
  N1               13                 34
  N2               13                 62
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    40   1
  13Q LOSS WILD-TYPE 152  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     40    1
  13Q LOSS WILD-TYPE  152   10
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               40                152
  1                1                 10
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    19  66
  13Q LOSS WILD-TYPE  88 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     19   66
  13Q LOSS WILD-TYPE   88  235
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               19                 88
  MALE                 66                235
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    74   5
  13Q LOSS WILD-TYPE 290  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     74    5
  13Q LOSS WILD-TYPE  290   15
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                74                290
  YES                5                 15
[1] 2 2
[1] FALSE
D66V9, continuous
D66V10, continuous
D66V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       5                         8    68
  13Q LOSS WILD-TYPE    38                        14   259
D66V12, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                8                 14
  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"
D66V13, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4  70
  13Q LOSS WILD-TYPE   5 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4   70
  13Q LOSS WILD-TYPE    5  299
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO               70                299
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    71  49
  14Q LOSS WILD-TYPE 156 129
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               120                285 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                49                129 
$`14Q LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20T TCGA-BT-A3PK 
      108.95        16.27        16.77        15.12        14.89         9.96 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IQ 
        4.90        15.12         2.14       130.88        87.32        17.72 
TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-E5-A4TZ 
       50.27        66.05        64.18        50.70       166.03        15.35 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A5C0 TCGA-FD-A5C1 
        0.92         1.22        29.16        46.78        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 
        6.28        62.86         6.15         3.06         4.31        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GU-AATP 
       17.23        11.08        17.62        70.32        19.13        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WU 
       19.82        20.28         8.58        19.07        22.72         3.45 
TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A9ST 
       35.97        14.24         1.84        33.14        51.32         4.21 
TCGA-XF-A9T0 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN2 
       26.27        54.90         7.63        98.99        44.32        61.45 
TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-2F-A9KP 
       86.30        13.64        94.29        19.69        24.13        11.97 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA87 
      104.65         8.35         0.62        41.75        51.16        47.80 
TCGA-5N-A9KI TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A2LB TCGA-CF-A1HR TCGA-CF-A1HS 
        2.50        19.04         5.06        16.18        12.79        12.56 
TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A8HY TCGA-CU-A5W6 TCGA-DK-A1A3 
       12.16        12.62        13.12        11.34         1.84        21.86 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-AA6U TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A6MD 
      112.44        17.95        19.00        38.83        22.16         4.24 
TCGA-E7-A6ME TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43U TCGA-G2-A2EF TCGA-G2-A3IE 
       24.03        25.74        22.98        20.91        61.94        20.12 
TCGA-G2-AA3B TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GU-A42Q TCGA-H4-A2HQ TCGA-HQ-A2OE 
       66.02        14.07         0.49        11.31        19.40        38.60 
TCGA-HQ-A2OF TCGA-K4-A6MB TCGA-KQ-A41R TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-SY-A9G5 
       64.01        15.42        44.38         1.15        12.23        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A9PD TCGA-UY-A9PE 
       17.62        37.05        22.68        69.34        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAMX 
        3.85         1.87        48.62        23.64        28.24         6.77 
TCGA-XF-AAN0 TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA51 TCGA-ZF-AA52 
       56.48        47.84        20.22         2.89        56.35        35.41 

$`14Q LOSS WILD-TYPE`
TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ 
       33.83        12.39        26.14         8.35        20.48        25.94 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E 
       28.70         8.98        18.58        12.92        18.48        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU 
       19.00        16.70        46.68         8.22        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
        9.67        17.98        53.29        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 
       36.66        38.24        52.01       165.73        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3B7 
       56.15        11.18        20.32        25.58        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A3SS 
       60.66        24.30        23.41        17.98        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35         3.62        15.58        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI 
        5.69         8.25        18.81        12.69        12.36         9.67 
TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       33.01        21.40        17.75        24.92        10.92        32.78 
TCGA-GV-A3QK TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       27.35         9.01        25.02         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE 
       52.73        50.56        46.98        86.83        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       12.76        11.90        21.04        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.10        13.74        10.82        11.31        71.57        91.73 
TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       30.94        18.58         3.88         9.63        21.11        30.28 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KQ 
        3.48        88.87        34.06        57.90        12.23        94.88 
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-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       66.54        10.22        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B 
        5.06        14.96         8.25        17.16         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF 
       36.43        28.41         1.94        23.01        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.13        13.08        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF 
        5.19        29.79        66.41        18.41        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
       20.81        10.55       163.30        15.02        13.58        18.81 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.35        12.03        43.59        29.72         5.36         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
       16.70         0.56         0.66        26.96        26.24        24.66 
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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
        5.52        14.96        19.33         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        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-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
        7.23         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
        2.20        18.97         7.63        20.05        15.78         4.73 
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-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        1.51        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81        16.27        11.80        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       13.48        16.67        16.54        76.01        78.25         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI 
      112.83        35.24        29.56        45.04         6.58        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9T4 TCGA-XF-AAME 
       64.80        79.66        66.41         5.98        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
      110.60         2.96         8.32        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4U 
       21.86        28.41        13.41        64.08        58.72         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       59.38        60.16        67.20        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.49               0.56 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            166.03             165.73 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            19.545             16.670 
[1] "0.5 - 166.0 (19.5)" "0.6 - 165.7 (16.7)"
[1] "hr=" "1.3"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED         0       36        39       45
  14Q LOSS WILD-TYPE       2       93       101       90
D67V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  0                  2
  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         37  55  19
  14Q LOSS WILD-TYPE       86 140  39
D67V4, multiclass
          clus
vv         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1+T2               37                 86
  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  33   3
  14Q LOSS WILD-TYPE 174  38  42   5
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               62                174
  N1                9                 38
  N2               33                 42
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    55   3
  14Q LOSS WILD-TYPE 137   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     55    3
  14Q LOSS WILD-TYPE  137    8
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               55                137
  1                3                  8
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    25  96
  14Q LOSS WILD-TYPE  82 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     25   96
  14Q LOSS WILD-TYPE   82  205
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               25                 82
  MALE                 96                205
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   112   3
  14Q LOSS WILD-TYPE 252  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    112    3
  14Q LOSS WILD-TYPE  252   17
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               112                252
  YES                3                 17
[1] 2 2
[1] FALSE
D67V9, continuous
D67V10, continuous
D67V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED      12                         5    98
  14Q LOSS WILD-TYPE    31                        17   229
D67V12, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                   12                 31
  BLACK OR AFRICAN AMERICAN                5                 17
  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"
D67V13, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     4 104
  14Q LOSS WILD-TYPE   5 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4  104
  14Q LOSS WILD-TYPE    5  265
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO              104                265
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    84  59
  15Q LOSS WILD-TYPE 143 119
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               143                262 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                59                119 
$`15Q LOSS MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C 
       16.27        15.12        26.14         8.35        20.48        28.70 
TCGA-C4-A0EZ TCGA-CU-A3KJ TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A6B2 TCGA-DK-A6B5 
        8.98        18.48        87.32         8.22        15.68        50.70 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 
       52.01       165.73       166.03        13.64        56.15        11.18 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A5BY TCGA-FD-A5C0 
       25.58         1.22        60.66        29.16         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
       58.92        12.69         4.31        31.07        17.23        11.08 
TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G 
       19.13        24.92        10.92        20.28         8.58        19.07 
TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB TCGA-KQ-A41P TCGA-R3-A69X TCGA-SY-A9G0 
       22.72        25.02         2.76        35.97        14.24        33.14 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       97.45        97.12        15.35         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAML 
       14.93        11.90        26.27         2.24        66.64         7.63 
TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA4T 
       98.99        61.45        13.64        30.28        88.87        19.69 
TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-5N-A9KI TCGA-5N-A9KM 
        8.35        27.62         0.62        51.16         2.50        17.42 
TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A42B 
       40.08         6.58        19.04         8.25        16.18        17.56 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A47X TCGA-DK-A1A7 TCGA-DK-A2I2 
       36.43         1.94        12.56        12.62        18.41         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ 
      142.78         8.15        15.02        12.03        43.59        22.16 
TCGA-E7-A7PW TCGA-FD-A3B3 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BZ 
       13.68        32.02        25.74        22.98         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TK TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IE 
        2.70        13.35        10.85        61.94        26.93        20.12 
TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 
       66.02        15.81         0.49         8.94         2.10         2.20 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE 
        7.63        15.78        19.10         8.48        19.40        38.60 
TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-KQ-A41R TCGA-LC-A66R 
       12.16         9.07        11.70        17.72        44.38        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       15.58        13.48        16.67        37.05        22.68        76.01 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH 
       35.24        29.56        17.82         6.21         3.85         1.87 
TCGA-XF-A9SG TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX 
       48.62         5.98        23.64       110.60         2.96         6.77 
TCGA-YF-AA3L TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4X 
       11.97        28.41        58.72        20.22         2.89        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       56.35        35.41        54.21        29.49        10.65 

$`15Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A3PJ 
      108.95        16.77        33.83        12.39        14.89        25.94 
TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E 
        9.96        18.58        12.92         4.90        15.12        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IQ 
        2.14        19.00        16.70       130.88        46.68        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L 
       64.18        53.29        76.60        67.36        36.66        38.24 
TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 
       13.64        20.32        15.35         0.92        33.04         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30        23.41        17.98        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35         3.62        15.58        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
        5.69         6.28        62.86        18.81         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
        3.06         9.67        33.01        17.62        70.32        21.40 
TCGA-GC-A3WC TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-HQ-A5ND 
       17.75        32.78        32.98        19.82        27.35         9.01 
TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q 
        3.45         9.14        27.68        52.73        50.56        46.98 
TCGA-S5-A6DX TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A9ST TCGA-XF-A9SV 
        1.84        86.83        51.32       125.49         4.21        12.76 
TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
       21.04        18.90         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 
       54.90        71.57        91.73        44.32        30.94        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       18.58         3.88         9.63        21.11        94.29         3.48 
TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       34.06        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
      104.65        44.94        16.83        17.16        34.98        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13I TCGA-BL-A13J 
       41.75        66.54        10.22        47.80         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.74        13.15        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42F TCGA-C4-A0F6 
       14.96         5.06        17.16         4.67        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-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD 
        5.19        29.79         1.84        21.86        66.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL 
       16.14        17.62        15.62        17.95         4.80        13.58 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       20.81        10.55       163.30        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        29.72         5.36         2.24        16.70 
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-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       24.66        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62O TCGA-FD-A6TF TCGA-FJ-A3Z9 
       14.96        20.91        19.33         7.10         2.27        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
       10.65         8.94         3.25        48.00        15.95        59.31 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
        7.23         6.94        29.36        20.71        15.91        14.07 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R 
       13.91        26.70         3.12        20.98        11.31        18.97 
TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QI 
       20.05         4.73         7.00        14.27        21.34        36.49 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        1.51        64.01        21.24         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-SY-A9G5 
       11.80         1.15        21.07        12.23        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HB 
       17.62        78.25        69.34         3.02       112.83        45.04 
TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SZ 
        6.58        17.88        64.80        79.66        66.41        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
       16.27        92.98         8.32        56.48        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       18.84         0.66        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA4V 
       21.86        13.41        64.08        47.84         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       60.16        19.40         8.52         5.52 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.49               0.56 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            166.03             163.30 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             17.82              17.62 
[1] "0.5 - 166.0 (17.8)" "0.6 - 163.3 (17.6)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         1       40        56       46
  15Q LOSS WILD-TYPE       1       89        84       89
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                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
  15Q LOSS MUTATED         36  77  17
  15Q LOSS WILD-TYPE       87 118  41
D68V4, multiclass
          clus
vv         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1+T2               36                 87
  T3                     77                118
  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
  15Q LOSS MUTATED    81  16  27   3
  15Q LOSS WILD-TYPE 155  31  48   5
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               81                155
  N1               16                 31
  N2               27                 48
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    52   4
  15Q LOSS WILD-TYPE 140   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     52    4
  15Q LOSS WILD-TYPE  140    7
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               52                140
  1                4                  7
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    42 102
  15Q LOSS WILD-TYPE  65 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     42  102
  15Q LOSS WILD-TYPE   65  199
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               42                 65
  MALE                102                199
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   131   4
  15Q LOSS WILD-TYPE 233  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    131    4
  15Q LOSS WILD-TYPE  233   16
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               131                233
  YES                4                 16
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, continuous
D68V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       6                         4   126
  15Q LOSS WILD-TYPE    37                        18   201
D68V12, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    6                 37
  BLACK OR AFRICAN AMERICAN                4                 18
  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"
D68V13, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     5 129
  15Q LOSS WILD-TYPE   4 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5  129
  15Q LOSS WILD-TYPE    4  240
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO              129                240
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    65  45
  16P LOSS WILD-TYPE 162 133
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               110                295 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                45                133 
$`16P LOSS MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A3PJ TCGA-CU-A0YN 
       16.27        16.77        15.12        26.14        25.94        12.92 
TCGA-CU-A3KJ TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3X2 TCGA-DK-A6B1 
       18.48       130.88        46.68        87.32        17.98        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A43Y 
       36.66        52.01       165.73        25.58        33.04        15.58 
TCGA-FD-A5BR TCGA-FD-A5C0 TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 
       26.73        18.08        12.69        12.36         4.31        31.07 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3JZ TCGA-GV-A6ZA TCGA-K4-A4AC TCGA-K4-A54R 
       24.92        10.92        19.82        22.72         9.14        27.68 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HF TCGA-XF-A8HG 
       50.56        35.97        33.14        86.83        97.12        15.35 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAN2 
       14.93         4.21        11.90        21.04         2.24        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA53 
       86.30        18.58        13.64        94.29        88.87        57.90 
TCGA-2F-A9KO TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BT-A20R TCGA-BT-A42E TCGA-CF-A1HS 
       24.13        10.22        40.08         5.06        36.43        12.56 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A2I4 TCGA-DK-A3WX TCGA-DK-AA6P 
        5.19         1.84        21.86       142.78        10.55        15.02 
TCGA-DK-AA76 TCGA-FD-A3B3 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BV 
       12.03        32.02         5.52        25.74        22.98         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-G2-A2EF TCGA-G2-A3IE 
       27.45         2.70         7.10        13.35        61.94        20.12 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
       15.91        14.07         8.94        26.70         2.10         2.20 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-K4-A5RH TCGA-K4-A5RI 
       19.10         8.48        36.49        38.60         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       17.72         1.81         1.15        15.58        13.48        12.23 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34       112.83        35.24        29.56         6.21         3.85 
TCGA-XF-A8HC TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9RF 
        6.58        79.66        23.64        56.48        11.97        64.08 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 
       47.84        20.22         2.89         8.61        67.20        56.35 
TCGA-ZF-AA54 TCGA-ZF-AA58 
       19.40        54.21 

$`16P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD 
      108.95        33.83        12.39        14.89         8.35        20.48 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR 
        9.96        28.70         8.98        18.58         4.90        15.12 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A3IQ 
       13.58         2.14        19.00        16.70         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV 
       50.27        21.30        23.21         9.67        66.05        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6S 
       53.29        76.60        15.68        50.70        38.24       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        0.92         1.22         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        29.16        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 
        3.62        53.88        10.78         5.69         8.25        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI 
        6.28        62.86        18.81         6.15         3.06         9.67 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       17.23        11.08        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK 
       19.13        17.75        32.78        32.98        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
        8.58        19.07         9.01        25.02         3.45         2.76 
TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A8HD 
       52.73        46.98        14.24         1.84        51.32        97.45 
TCGA-XF-A8HE TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SV TCGA-XF-A9T0 
      125.49         3.22        15.98        34.45        12.76        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90         7.63        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE 
       30.94         3.88         9.63        21.11        30.28         3.48 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       34.06        19.69        12.23        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 
       50.04         0.62        41.75        51.16        66.54        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
        2.50        17.42         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U 
       13.15        19.04        12.16        17.88        19.50        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF 
       28.41         1.94        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-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-DK-A1A6 
       11.34        11.34        11.87        13.08        29.79        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY 
        7.79         4.80        13.58         8.15        20.81       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 
       13.58        18.81        19.00        15.35        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        22.16         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-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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A43S 
       16.77         8.94        12.62        22.52        27.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       20.91        19.33         2.27        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-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.23        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R 
        0.49        13.91         3.12        20.98        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
       21.34         1.51        19.40        64.01        12.16        21.24 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A8JT 
       15.42        16.27        11.80        44.38        15.32        21.07 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HH 
       76.01        78.25         3.02        17.82        45.04         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ 
       17.88        48.62        64.80        66.41         5.98        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       16.27        92.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG 
       31.20        35.84        21.86        28.41        13.41        58.72 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       59.38        60.16        35.41         8.52        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              1.15               0.49 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            165.73             166.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             19.61              17.16 
[1] "1.1 - 165.7 (19.6)" "0.5 - 166.0 (17.2)"
[1] "hr=" "1.3"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         1       31        39       38
  16P LOSS WILD-TYPE       1       98       101       97
D69V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                31                 98
  STAGE III               39                101
  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
  16P LOSS MUTATED         28  63  10
  16P LOSS WILD-TYPE       95 132  48
D69V4, multiclass
          clus
vv         16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1+T2               28                 95
  T3                     63                132
  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
  16P LOSS MUTATED    54  15  22   2
  16P LOSS WILD-TYPE 182  32  53   6
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               54                182
  N1               15                 32
  N2               22                 53
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    39   2
  16P LOSS WILD-TYPE 153   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     39    2
  16P LOSS WILD-TYPE  153    9
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               39                153
  1                2                  9
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    27  83
  16P LOSS WILD-TYPE  80 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     27   83
  16P LOSS WILD-TYPE   80  218
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               27                 80
  MALE                 83                218
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   100   2
  16P LOSS WILD-TYPE 264  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    100    2
  16P LOSS WILD-TYPE  264   18
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO               100                264
  YES                2                 18
[1] 2 2
[1] FALSE
D69V9, continuous
D69V10, continuous
D69V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       4                         3    98
  16P LOSS WILD-TYPE    39                        19   229
D69V12, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                3                 19
  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"
D69V13, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  98
  16P LOSS WILD-TYPE   6 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   98
  16P LOSS WILD-TYPE    6  271
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               98                271
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    61  46
  16Q LOSS WILD-TYPE 166 132
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               107                298 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                46                132 
$`16Q LOSS MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-CU-A0YN TCGA-DK-A1AC TCGA-DK-A2HX 
       16.27        16.77        15.12        12.92       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M 
       87.32         9.67        17.98        67.36        36.66        52.01 
TCGA-DK-AA6R TCGA-DK-AA6W TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3SS TCGA-FD-A5BR 
      165.73        13.64        15.35        25.58        12.85        26.73 
TCGA-FD-A5C0 TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-GU-A42P 
       18.08        12.69        12.36        31.07        11.08        10.92 
TCGA-GV-A3JZ TCGA-K4-A4AC TCGA-KQ-A41O TCGA-KQ-A41P TCGA-SY-A9G0 TCGA-UY-A78N 
       19.82         9.14        50.56        35.97        33.14        86.83 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9ST 
      125.49        97.12        15.35         3.22        14.93         4.21 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAML TCGA-XF-AAN2 TCGA-XF-AAN3 
       11.90        21.04         2.24         7.63        61.45        86.30 
TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4T TCGA-ZF-AA53 
       18.58        13.64        30.28        94.29        19.69        57.90 
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BT-A42E TCGA-CF-A1HS TCGA-CU-A3QU 
       41.75        10.22        40.08        36.43        12.56         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A2I4 TCGA-DK-AA6P TCGA-DK-AA76 TCGA-E7-A4IJ 
        1.84        21.86       142.78        15.02        12.03        22.16 
TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
        5.52        22.98        20.91         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OP 
        7.10        13.35        20.12        15.91        14.07         2.10 
TCGA-GD-A6C6 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OE 
        2.20        14.27        19.10         8.48        36.49        38.60 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41R 
       21.24         9.07        11.70        17.72         1.81        44.38 
TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A8OB TCGA-UY-A8OD 
        1.15        15.58        13.48        12.23        69.34       112.83 
TCGA-UY-A9PA TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-AAMG 
       35.24         3.85         6.58        79.66        23.64       110.60 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN 
        6.77        56.48        11.97        64.08        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA58 
        2.89         8.61        67.20        56.35        54.21 

$`16Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
      108.95        33.83        12.39        26.14        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL 
       20.48        25.94         9.96        28.70         8.98        18.58 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
        4.90        15.12        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       16.70         8.22        17.72        50.27        21.30        23.21 
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-AA6S TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
       38.24       166.03        13.64        56.15        11.18        20.32 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P 
       23.41        17.98        29.16        46.78        19.79        27.35 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        15.58        53.88        10.78         5.69         8.25 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG 
       58.92         6.28        62.86        18.81         6.15         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
        4.31         9.67        17.23        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP 
       21.40        19.13        17.75        24.92        32.78        32.98 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q 
       25.02         3.45         2.76        27.68        52.73        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A9SK TCGA-XF-A9SM 
       14.24         1.84        51.32        97.45        15.98        34.45 
TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       12.76        26.27        18.90        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       10.82        11.31        54.90        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RE 
       44.32        30.94         3.88         9.63        21.11         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       88.87        34.06        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 
       27.62        50.04         0.62        51.16        66.54        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
        2.50        17.42         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       17.56        28.41         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-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL 
       12.10        11.34        11.34        11.87        13.08        29.79 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
       17.95         7.79         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
       10.55       163.30        13.58        18.81        19.00        15.35 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       43.59        38.83        29.72         5.36         2.24        16.70 
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-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-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A6TF TCGA-FD-A6TK 
       27.98        25.74        14.96        19.33         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C 
       15.95        26.93        59.31         7.23        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       29.36        20.71        15.81         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       26.70         3.12        20.98        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-H4-A2HO 
       20.05        15.78         4.73         7.00        21.34         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       19.40        64.01        12.16        15.42        16.27        11.80 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       15.32        21.07        16.67        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PB 
       37.05        22.68        76.01        78.25         3.02        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         6.21        45.04         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       64.80        66.41         5.98        28.24        16.27        92.98 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        2.96         8.32        27.06        75.39        18.84         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA54 
       13.41        58.72        59.38        60.16        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        29.49         5.52        10.65 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              1.15               0.49 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            165.73             166.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             18.08              17.59 
[1] "1.1 - 165.7 (18.1)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         1       33        33       39
  16Q LOSS WILD-TYPE       1       96       107       96
D70V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                  1
  STAGE II                33                 96
  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
  16Q LOSS MUTATED         30  55  14
  16Q LOSS WILD-TYPE       93 140  44
D70V4, multiclass
          clus
vv         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1+T2               30                 93
  T3                     55                140
  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
  16Q LOSS MUTATED    49  13  24   3
  16Q LOSS WILD-TYPE 187  34  51   5
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               49                187
  N1               13                 34
  N2               24                 51
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    38   2
  16Q LOSS WILD-TYPE 154   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     38    2
  16Q LOSS WILD-TYPE  154    9
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               38                154
  1                2                  9
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    25  82
  16Q LOSS WILD-TYPE  82 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     25   82
  16Q LOSS WILD-TYPE   82  219
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               25                 82
  MALE                 82                219
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    97   3
  16Q LOSS WILD-TYPE 267  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     97    3
  16Q LOSS WILD-TYPE  267   17
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                97                267
  YES                3                 17
[1] 2 2
[1] FALSE
D70V9, continuous
D70V10, continuous
D70V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       5                         4    94
  16Q LOSS WILD-TYPE    38                        18   233
D70V12, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   94                233
[1] 3 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  93
  16Q LOSS WILD-TYPE   4 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   93
  16Q LOSS WILD-TYPE    4  276
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  4
  NOT HISPANIC OR LATINO               93                276
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    93  88
  17P LOSS WILD-TYPE 134  90
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               181                224 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                88                 90 
$`17P LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A3PK 
      108.95        16.27        12.39        26.14        14.89         9.96 
TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       18.48        16.70        46.68        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       50.27        21.30         9.67        66.05        17.98        64.18 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-E5-A4TZ TCGA-E7-A541 
       50.70        38.24       165.73       166.03        15.35        25.58 
TCGA-E7-A7DU TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS 
        0.92        60.66        24.30        29.16        46.78        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TA 
       27.35         3.62        26.73         8.25         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       18.81        12.69         3.06        17.62        70.32        21.40 
TCGA-GC-A3YS TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A4AC 
       24.92        32.98        20.28         8.58         9.01         9.14 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       52.73        50.56        46.98        14.24         1.84        33.14 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       51.32        97.45       125.49        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9T3 TCGA-XF-AAMF 
       15.98        14.93         4.21        12.76         2.24        10.82 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-YF-AA3M 
       54.90        91.73        44.32        30.94        86.30        13.64 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KR TCGA-4Z-AA80 
        3.48        88.87        19.69        57.90       104.65         0.62 
TCGA-4Z-AA82 TCGA-5N-A9KM TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20X 
       51.16        17.42        19.04        17.88        19.50         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HR 
       17.16        16.18         4.67        36.43         1.94        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A5W6 
       12.56        13.97        12.13        12.16        12.62         1.84 
TCGA-DK-A1AD TCGA-DK-A3IL TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
      112.44        13.58        13.58        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A6ME 
       43.59        38.83        22.16        26.96         4.24        24.03 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3SO 
       13.68        12.95         8.09        16.77         8.94         5.52 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK 
       22.98        20.91         5.36         7.10        13.35        10.85 
TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       10.65        61.94        48.00        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A6C6 
       20.12        14.07         0.49        13.91         2.10         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW 
       11.31        18.97         7.63         4.73         7.00        21.34 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB 
       19.40        64.01        12.16        11.70        17.72        15.42 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78M 
       11.80         1.15        12.23        16.67        38.99        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        78.25         3.02       112.83        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SX 
        3.85         1.87        48.62        79.66         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
       28.24         2.96         8.32         6.77        56.48        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RG 
       22.36        25.41        31.20        21.86        28.41        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 
       47.84        20.22         2.89        60.16        56.35        19.40 
TCGA-ZF-AA56 
        8.52 

$`17P LOSS WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ 
       16.77        15.12        33.83         8.35        20.48        25.94 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       28.70         8.98        18.58        12.92         4.90        15.12 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A3IU TCGA-DK-A6AW 
       13.58         2.14        19.00       130.88        23.21        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6W 
       76.60        67.36        15.68        36.66        52.01        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A7DV TCGA-FD-A3B6 
       13.64        56.15        11.18        20.32         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BS 
        4.01        23.41        17.98        19.79        15.58        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TE 
       10.78         5.69        18.08        58.92         6.15        12.36 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QK 
       19.13        17.75        10.92        32.78        19.82        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R 
       19.07        22.72        25.02         3.45         2.76        27.68 
TCGA-KQ-A41P TCGA-UY-A78N TCGA-XF-A9SM TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       35.97        86.83        34.45        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAML 
       18.90        66.64         2.10        13.74        11.31         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       71.57        98.99        61.45        18.58         3.88         9.63 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KO 
       21.11        30.28        94.29        34.06        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       11.97        94.88         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 
       34.98        27.62        50.04        41.75        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80         2.50        40.08         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
        6.58        13.15        12.16         5.06        14.96         5.06 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S 
       17.56        28.41        23.01        12.59        13.08        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.34        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF 
       29.79        21.86        66.41        18.41        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
       15.62        17.95         7.79       142.78         4.80         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-E7-A3X6 
       20.81        10.55       163.30        15.02        18.81        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 
        5.36         2.24        16.70         0.56         0.66        26.24 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B8 
       24.66        14.07        15.32        14.37        32.02        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BZ 
       22.52        27.98        25.74        14.96        19.33        27.45 
TCGA-FD-A62N TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK 
        2.70         2.27        12.66         8.94         3.25        15.95 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A764 TCGA-GU-A766 
        8.94        26.70         3.12        20.98        20.05        15.78 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE 
       14.27        19.10         8.48        36.49         1.51        38.60 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41R TCGA-LC-A66R 
       21.24         9.07         1.81        16.27        44.38        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L 
       15.58        21.07        13.48        16.54        17.62        37.05 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI 
       69.34        35.24        29.56        45.04         6.58        17.88 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAN4 
       64.80        66.41        16.27        92.98       110.60        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       75.39        18.84         0.66        35.84        13.41        64.08 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H 
        8.61        59.38        67.20        35.41        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.49               0.56 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            166.03             163.30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             17.72              17.59 
[1] "0.5 - 166.0 (17.7)" "0.6 - 163.3 (17.6)"
[1] "hr=" "1.2"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         0       53        64       65
  17P LOSS WILD-TYPE       2       76        76       70
D71V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                53                 76
  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    97  20  40   3
  17P LOSS WILD-TYPE 139  27  35   5
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               97                139
  N1               20                 27
  N2               40                 35
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    78   3
  17P LOSS WILD-TYPE 114   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     78    3
  17P LOSS WILD-TYPE  114    8
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               78                114
  1                3                  8
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    51 131
  17P LOSS WILD-TYPE  56 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     51  131
  17P LOSS WILD-TYPE   56  170
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               51                 56
  MALE                131                170
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   162   8
  17P LOSS WILD-TYPE 202  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    162    8
  17P LOSS WILD-TYPE  202   12
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               162                202
  YES                8                 12
[1] 2 2
[1] FALSE
D71V9, continuous
D71V10, continuous
D71V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED      16                        11   143
  17P LOSS WILD-TYPE    27                        11   184
D71V12, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                   16                 27
  BLACK OR AFRICAN AMERICAN               11                 11
  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"
D71V13, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4 166
  17P LOSS WILD-TYPE   5 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  166
  17P LOSS WILD-TYPE    5  203
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO              166                203
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    24  22
  17Q LOSS WILD-TYPE 203 156
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                46                359 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                156 
$`17Q LOSS MUTATED`
TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A6AV TCGA-E5-A4TZ TCGA-FD-A3NA TCGA-FD-A3SS 
       16.70         8.22        64.18        15.35        60.66        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-GC-A3YS TCGA-K4-A4AC TCGA-SY-A9G0 TCGA-XF-A9SP 
       27.35         3.62        24.92         9.14        33.14        14.93 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-4Z-AA82 TCGA-BT-A20P TCGA-BT-A2LA TCGA-CF-A1HR 
       19.69        57.90        51.16        17.88        17.16        12.79 
TCGA-CF-A1HS TCGA-CF-A3MI TCGA-DK-AA6Q TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A97Q 
       12.56        12.16        13.58        12.03        38.83         8.09 
TCGA-FD-A43U TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A3IB TCGA-G2-A3IE 
       20.91        13.35        10.85        10.65         7.23        20.12 
TCGA-GD-A3OP TCGA-GU-A762 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-HQ-A2OF TCGA-PQ-A6FN 
        2.10         7.63         7.00        21.34        64.01        16.67 
TCGA-SY-A9G5 TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A9SI TCGA-XF-AAMX 
       38.99        17.82         6.21         3.85        79.66         6.77 
TCGA-ZF-A9R3 TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       31.20        47.84        20.22         2.89 

$`17Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       28.70         8.98        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A2HX 
       18.48        13.58         2.14        19.00       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       87.32        17.72        50.27        21.30        23.21         9.67 
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-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 
       13.64        13.64        56.15        11.18        20.32        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL 
        0.92         1.22        33.04         4.01        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BR 
       17.98        29.16        46.78        19.79        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       33.01        17.62        70.32        21.40        19.13        17.75 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        2.76        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
       14.24         1.84        86.83        51.32        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST 
       97.12        15.35         3.22        15.98        34.45         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         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-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-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       13.15        19.04        12.16        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        5.06         8.25        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       28.41         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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
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-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
       20.81        10.55       163.30        15.02        18.81        19.00 
TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        43.59        29.72         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       24.03        24.66        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU 
       27.98         5.52        25.74        22.98        14.96        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TF TCGA-FJ-A3Z9 
        5.36        27.45         2.70         7.10         2.27        12.66 
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-A2EO TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       59.31        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.91        14.07         0.49         8.94        13.91        26.70 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 
        3.12        20.98         2.20        11.31        18.97        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
       15.78         4.73        14.27        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
        1.51        19.40        38.60        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
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-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       12.23        16.54        17.62        37.05        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        35.24        29.56 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       45.04         6.58         1.87        17.88        48.62        64.80 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
      110.60         2.96         8.32        56.48        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R5 
       18.84         0.66        11.97        22.36        25.41        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4U 
       21.86        28.41        13.41        64.08        58.72         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
       59.38        60.16        67.20        56.35        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21        29.49         5.52        10.65 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              2.10               0.49 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             79.66             166.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             16.01              17.75 
[1] "2.1 - 79.7 (16.0)"  "0.5 - 166.0 (17.8)"
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED         0       16        15       15
  17Q LOSS WILD-TYPE       2      113       125      120
D72V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                16                113
  STAGE III               15                125
  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
  17Q LOSS MUTATED         14  16  11
  17Q LOSS WILD-TYPE      109 179  47
D72V4, multiclass
          clus
vv         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1+T2               14                109
  T3                     16                179
  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
  17Q LOSS MUTATED    24   4   8   3
  17Q LOSS WILD-TYPE 212  43  67   5
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               24                212
  N1                4                 43
  N2                8                 67
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    18   1
  17Q LOSS WILD-TYPE 174  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     18    1
  17Q LOSS WILD-TYPE  174   10
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               18                174
  1                1                 10
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    15  31
  17Q LOSS WILD-TYPE  92 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     15   31
  17Q LOSS WILD-TYPE   92  270
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               15                 92
  MALE                 31                270
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    41   3
  17Q LOSS WILD-TYPE 323  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     41    3
  17Q LOSS WILD-TYPE  323   17
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                41                323
  YES                3                 17
[1] 2 2
[1] FALSE
D72V9, continuous
D72V10, continuous
D72V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       5                         5    34
  17Q LOSS WILD-TYPE    38                        17   293
D72V12, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    5                 38
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                   34                293
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  44
  17Q LOSS WILD-TYPE   9 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   44
  17Q LOSS WILD-TYPE    9  325
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               44                325
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    52  46
  18P LOSS WILD-TYPE 175 132
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                98                307 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                46                132 
$`18P LOSS MUTATED`
TCGA-BT-A20N TCGA-BT-A20T TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A2HX 
       26.14        14.89        13.58         2.14        16.70        46.68 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 
       17.72        50.27        21.30        17.98        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA77 TCGA-E7-A7DV TCGA-FD-A3B7 
       50.70        38.24       166.03        20.32         1.22         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A6TA TCGA-GC-A3BM TCGA-GC-A3YS 
       24.30        29.16        46.78        62.86        21.40        24.92 
TCGA-GV-A40E TCGA-KQ-A41P TCGA-SY-A9G0 TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-AAMR 
        8.58        35.97        33.14        11.90        66.64        91.73 
TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-AA4T TCGA-2F-A9KO 
       44.32        86.30        13.64        21.11        19.69        24.13 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA82 
       94.88       104.65         8.35        34.98        27.62        51.16 
TCGA-4Z-AA83 TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42B 
       66.54        19.04         5.06         8.25        17.16        17.56 
TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.79        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A8HY TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AF 
       11.34         1.84        21.86        18.41       112.44        17.62 
TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-AA6P TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A5KE 
       17.95        13.58        15.02        43.59        29.72         0.56 
TCGA-E7-A6MD TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A62O TCGA-FD-A62S TCGA-G2-A3IE 
        4.24        12.95         8.09         7.10        13.35        20.12 
TCGA-G2-AA3B TCGA-GC-A3RD TCGA-GU-A764 TCGA-GU-A767 TCGA-GV-A3JW TCGA-HQ-A2OE 
       66.02        14.07        20.05         4.73        21.34        38.60 
TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 
       64.01        11.70        17.72        12.23        16.67        38.99 
TCGA-UY-A78M TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-AAMW TCGA-YC-A89H TCGA-YF-AA3L 
       22.68         6.21         3.85         8.32        18.84        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N 
       22.36        28.41        13.41        58.72        47.84         2.89 
TCGA-ZF-AA4U TCGA-GU-AATO 
        8.61        10.65 

$`18P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        20.48        25.94         9.96        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1AA 
       18.58        12.92         4.90        15.12        18.48        19.00 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
      130.88        87.32         8.22        23.21         9.67        66.05 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R 
       53.29        76.60        67.36        36.66        52.01       165.73 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        13.64        56.15        11.18        15.35        25.58 
TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR 
        0.92        33.04        60.66        23.41        17.98        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       12.85        27.35         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       10.78         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        9.67        31.07        17.23        11.08        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       70.32        19.13        17.75        10.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       19.82        20.28        27.35        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A78N TCGA-UY-A9PH 
       50.56        46.98        14.24         1.84        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       97.45       125.49        97.12        15.35         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 
       34.45        14.93         4.21        12.76        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
       18.90         2.24         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
       54.90         7.63        71.57        98.99        30.94        61.45 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       18.58         3.88         9.63        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-4Z-AA7N 
       88.87        34.06        57.90        12.23        11.97        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 
       16.83        17.16        50.04         0.62        41.75        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-BT-A42F 
       14.96         5.06        16.18         4.67        36.43        28.41 
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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 
       11.34        11.87        13.08         5.19        29.79        66.41 
TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
       16.14        15.62         7.79       142.78         4.80         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       20.81        10.55       163.30        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        12.03        38.83         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
       16.70         0.66        26.96        26.24        24.03        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       13.68        14.07        15.32        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        2.70         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
        7.23         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
        0.49         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 
       20.98         2.20        11.31        18.97         7.63        15.78 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
        7.00        14.27        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A6MB 
       19.40        12.16        21.24         9.07         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O 
       21.07        13.48        16.54        17.62        37.05        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        35.24        29.56 
TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82        45.04         6.58         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 
       16.27        92.98       110.60         2.96         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       27.06        75.39         0.66        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       21.86        64.08        20.22        59.38        60.16        67.20 
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        29.49 
TCGA-ZF-AA5N 
        5.52 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.56               0.49 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            166.03             165.73 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            18.195             17.160 
[1] "0.6 - 166.0 (18.2)" "0.5 - 165.7 (17.2)"
[1] "hr=" "1"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         0       31        24       42
  18P LOSS WILD-TYPE       2       98       116       93
D73V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                31                 98
  STAGE III               24                116
  STAGE IV                42                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1+T2  T3  T4
  18P LOSS MUTATED         33  47  13
  18P LOSS WILD-TYPE       90 148  45
D73V4, multiclass
          clus
vv         18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1+T2               33                 90
  T3                     47                148
  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
  18P LOSS MUTATED    47  12  27   3
  18P LOSS WILD-TYPE 189  35  48   5
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               47                189
  N1               12                 35
  N2               27                 48
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    51   1
  18P LOSS WILD-TYPE 141  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     51    1
  18P LOSS WILD-TYPE  141   10
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               51                141
  1                1                 10
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    29  69
  18P LOSS WILD-TYPE  78 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     29   69
  18P LOSS WILD-TYPE   78  232
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               29                 78
  MALE                 69                232
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    86   5
  18P LOSS WILD-TYPE 278  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     86    5
  18P LOSS WILD-TYPE  278   15
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                86                278
  YES                5                 15
[1] 2 2
[1] FALSE
D73V9, continuous
D73V10, continuous
D73V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED      11                         4    77
  18P LOSS WILD-TYPE    32                        18   250
D73V12, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                   11                 32
  BLACK OR AFRICAN AMERICAN                4                 18
  WHITE                                   77                250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  86
  18P LOSS WILD-TYPE   6 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   86
  18P LOSS WILD-TYPE    6  283
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  6
  NOT HISPANIC OR LATINO               86                283
[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 141 118
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               146                259 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                60                118 
$`18Q LOSS MUTATED`
TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-CU-A0YN TCGA-CU-A0YR 
       16.27        26.14        14.89         8.35        12.92        15.12 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ 
       13.58         2.14        16.70        46.68        87.32        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
       50.27        21.30        66.05        64.18        15.68        50.70 
TCGA-DK-AA6M TCGA-DK-AA6S TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SN 
       52.01       166.03         1.22         4.01        60.66        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A6TA TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GC-A3YS 
       46.78        12.85        62.86        17.23        21.40        24.92 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-KQ-A41P TCGA-SY-A9G0 
        8.58        19.07        22.72        25.02        35.97        33.14 
TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SW TCGA-XF-A9T5 
       97.12         3.22        15.98        14.93        11.90        66.64 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3M 
       54.90        71.57        91.73        44.32        86.30        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KQ 
       21.11        88.87        19.69        57.90        24.13        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA82 
      104.65         8.35        17.16        34.98        27.62        51.16 
TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20X 
       66.54         2.50        17.42        19.04         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A42B TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI 
       17.16        17.56        12.79        12.56        12.13        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A5W6 
       10.95        12.66        11.34        11.34        11.87         1.84 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL 
       18.41       112.44        17.62        17.95         4.80        13.58 
TCGA-DK-AA6P TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A5KE TCGA-E7-A6MD 
       15.02        15.35        43.59        29.72         0.56         4.24 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.95         8.09        16.77         5.52        25.74        22.98 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-AA3B 
        2.70         7.10        13.35        61.94        20.12        66.02 
TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GD-A3OS 
       29.36        15.91        14.07         0.49         2.10        20.98 
TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW 
        2.20         7.63        20.05        15.78         4.73        21.34 
TCGA-GV-A3JX TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI 
       19.10        19.40        38.60        64.01        21.24        11.70 
TCGA-K4-A5RJ TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       17.72         1.15        15.32        13.48        12.23        16.67 
TCGA-SY-A9G5 TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A9SX TCGA-XF-AAMG 
       38.99         6.21         3.85         6.58        23.64       110.60 
TCGA-XF-AAMT TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG 
        2.96        11.97        22.36        28.41        13.41        58.72 
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-AA5H TCGA-GU-AATO 
       29.49        10.65 

$`18Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A2LD 
      108.95        16.77        15.12        33.83        12.39        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO 
       25.94         9.96        28.70         8.98        18.58         4.90 
TCGA-CU-A3KJ TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV 
       18.48        19.00       130.88         8.22        23.21         9.67 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L 
       17.98        53.29        76.60        67.36        36.66        38.24 
TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      165.73        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL 
       15.35        25.58         0.92        33.04        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       17.98        19.79        27.35         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        18.81         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        4.31         9.67        31.07        11.08        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       70.32        19.13        17.75        10.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB 
       19.82        20.28        27.35         9.01         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X 
        9.14        27.68        52.73        50.56        46.98        14.24 
TCGA-S5-A6DX TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        1.84        86.83        51.32        97.45       125.49        15.35 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       34.45         4.21        12.76        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML 
        2.24         2.10        13.74        10.82        11.31         7.63 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       98.99        30.94        61.45        18.58         3.88         9.63 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KP 
       30.28        94.29         3.48        34.06        12.23        11.97 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 
       44.94        16.83        50.04         0.62        41.75        10.22 
TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       47.80        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V 
       13.15        12.16        17.88        19.50        14.96         5.06 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
       16.18         4.67        36.43        28.41         1.94        23.01 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       13.97        12.59        13.08        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A3QU 
       12.26        13.12        12.00        12.10        13.08         5.19 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I2 
       29.79        21.86        66.41        16.14        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q 
      142.78         8.15        20.81        10.55       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       18.81        19.00        12.03        38.83         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
        2.24        16.70         0.66        26.96        26.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
       24.66        13.68        14.07        15.32        14.37        32.02 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A43S TCGA-FD-A43U 
        8.94        12.62        22.52        27.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
       19.33         5.36        27.45         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       10.65         8.94         3.25        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 
       59.31         7.23         6.94        20.71        15.81         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-AATQ 
       13.91        26.70         3.12        11.31        18.97         7.00 
TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A5RH 
       14.27         8.48        36.49         1.51        12.16         9.07 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A5Z6 
        1.81        15.42        16.27        11.80        44.38        15.58 
TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       21.07        16.54        17.62        37.05        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        35.24        29.56 
TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       17.82        45.04         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       79.66        66.41         5.98        28.24        16.27        92.98 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
        8.32         6.77        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RF 
        0.66        25.41        31.20        35.84        21.86        64.08 
TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       20.22        59.38        67.20        19.40         8.52        54.21 
TCGA-ZF-AA5N 
        5.52 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.49               0.62 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            166.03             165.73 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             17.59              17.75 
[1] "0.5 - 166.0 (17.6)" "0.6 - 165.7 (17.8)"
[1] "hr=" "1.2"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         0       45        47       53
  18Q LOSS WILD-TYPE       2       84        93       82
D74V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                45                 84
  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         43  70  23
  18Q LOSS WILD-TYPE       80 125  35
D74V4, multiclass
          clus
vv         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1+T2               43                 80
  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 158  32  42   4
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               78                158
  N1               15                 32
  N2               33                 42
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    71   2
  18Q LOSS WILD-TYPE 121   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     71    2
  18Q LOSS WILD-TYPE  121    9
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               71                121
  1                2                  9
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    43 103
  18Q LOSS WILD-TYPE  64 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     43  103
  18Q LOSS WILD-TYPE   64  198
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               43                 64
  MALE                103                198
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   132   5
  18Q LOSS WILD-TYPE 232  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    132    5
  18Q LOSS WILD-TYPE  232   15
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               132                232
  YES                5                 15
[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    50  45
  19P LOSS WILD-TYPE 177 133
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                95                310 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                45                133 
$`19P LOSS MUTATED`
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A1A5 TCGA-DK-A2I6 
       20.48         9.96         8.98        12.92         2.14        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-E7-A7DV TCGA-FD-A3SJ 
        8.22        17.72        21.30        17.98         1.22        24.30 
TCGA-FD-A3SM TCGA-FD-A3SS TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TB 
       17.98        12.85         8.25        18.08        58.92        18.81 
TCGA-FD-A6TE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3RB TCGA-GU-A42P 
       12.36        17.23        11.08        33.01        19.13        10.92 
TCGA-GV-A3JZ TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A54R TCGA-KQ-A41Q TCGA-R3-A69X 
       19.82         9.01        25.02        27.68        46.98        14.24 
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-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R 
       86.30        13.64        30.28        94.29        88.87        34.06 
TCGA-ZF-AA53 TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-5N-A9KI TCGA-BT-A20R TCGA-BT-A20V 
       57.90         8.35        27.62         2.50         5.06         5.06 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-DK-A1AD 
       16.18         4.67        17.56        36.43        23.01       112.44 
TCGA-DK-A3IL TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A85H TCGA-E7-A97P 
       13.58        15.35        43.59        22.16        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FJ-A3ZE 
        8.09         5.52        22.98         5.36        27.45        10.65 
TCGA-FJ-A871 TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        8.94         7.23        20.12         6.94        29.36        20.71 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-H4-A2HQ 
        0.49         8.94         2.20        11.31         7.63        19.40 
TCGA-K4-A5RJ TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       17.72         1.15        15.32        13.48        12.23        16.67 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB 
       38.99        22.68       112.83        17.82         3.85        45.04 
TCGA-XF-A9SG TCGA-XF-AAMG TCGA-XF-AAMX TCGA-ZF-AA5H TCGA-GU-AATO 
       48.62       110.60         6.77        29.49        10.65 

$`19P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42C TCGA-CF-A9FL 
       26.14        14.89         8.35        25.94        28.70        18.58 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB 
        4.90        15.12        18.48        13.58        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
      130.88        46.68        50.27        23.21         9.67        66.05 
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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       36.66        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        56.15        11.18        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SN 
        0.92        33.04         4.01        60.66        23.41        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       46.78        19.79        27.35         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC 
       53.88        10.78         5.69         6.28        62.86         6.15 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A3VY 
       12.69         3.06         4.31         9.67        31.07        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP 
       70.32        21.40        17.75        24.92        32.78        32.98 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WU 
       20.28        27.35         8.58        19.07        22.72         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-S5-A6DX 
        2.76         9.14        52.73        50.56        35.97         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       33.14        86.83        51.32        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 
       15.35        15.98        14.93        12.76        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       18.90         2.24        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
        7.63        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RE 
       61.45        18.58         3.88         9.63        21.11         3.48 
TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       19.69        12.23        24.13        11.97        94.88       104.65 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        17.16        34.98        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM 
       41.75        51.16        66.54        10.22        47.80        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X 
       19.04        12.16        17.88        19.50        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       17.16        28.41         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-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.34        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE 
       29.79         1.84        21.86        66.41        18.41        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        8.15        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       18.81        19.00        12.03        38.83        29.72         5.36 
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-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
        4.24        24.03        24.66        13.68        14.07        15.32 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A62O 
       25.74        14.96        20.91        19.33         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EF 
       13.35         2.27        10.85        12.66         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GC-A3OO 
       48.00        15.95        26.93        59.31        66.02        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.91        14.07        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       20.98        18.97        20.05        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
       14.27        21.34        19.10         8.48        36.49         1.51 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A5Z6 
        1.81        15.42        16.27        11.80        44.38        15.58 
TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P 
       21.07        16.54        17.62        37.05        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HC 
       69.34         3.02        35.24        29.56         6.21         6.58 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
        1.87        17.88        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW 
       23.64        28.24        16.27        92.98         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
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-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       19.40         8.52        54.21         5.52 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.49               0.56 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            112.83             166.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             16.67              17.88 
[1] "0.5 - 112.8 (16.7)" "0.6 - 166.0 (17.9)"
[1] "hr=" "1.3"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         0       20        36       39
  19P LOSS WILD-TYPE       2      109       104       96
D75V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                20                109
  STAGE III               36                104
  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
  19P LOSS MUTATED         19  56  13
  19P LOSS WILD-TYPE      104 139  45
D75V4, multiclass
          clus
vv         19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1+T2               19                104
  T3                     56                139
  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
  19P LOSS MUTATED    45  14  19   5
  19P LOSS WILD-TYPE 191  33  56   3
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               45                191
  N1               14                 33
  N2               19                 56
  N3                5                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    26  69
  19P LOSS WILD-TYPE  81 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     26   69
  19P LOSS WILD-TYPE   81  232
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               26                 81
  MALE                 69                232
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    88   1
  19P LOSS WILD-TYPE 276  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     88    1
  19P LOSS WILD-TYPE  276   19
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                88                276
  YES                1                 19
[1] 2 2
[1] FALSE
D75V9, continuous
D75V10, continuous
D75V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       4                         5    80
  19P LOSS WILD-TYPE    39                        17   247
D75V12, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    4                 39
  BLACK OR AFRICAN AMERICAN                5                 17
  WHITE                                   80                247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V13, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     4  85
  19P LOSS WILD-TYPE   5 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4   85
  19P LOSS WILD-TYPE    5  284
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  5
  NOT HISPANIC OR LATINO               85                284
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    30  29
  19Q LOSS WILD-TYPE 197 149
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                59                346 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                29                149 
$`19Q LOSS MUTATED`
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A3IN TCGA-DK-A3IQ 
       20.48         9.96         8.98        12.92         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FT-A61P 
       21.30        17.98         8.25        58.92        12.36        11.08 
TCGA-G2-A2ES TCGA-GC-A3RB TCGA-K4-A54R TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW 
       33.01        19.13        27.68        34.45         4.21        11.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-2F-A9KW 
       66.64         2.10         7.63        30.28        88.87         8.35 
TCGA-4Z-AA7W TCGA-5N-A9KI TCGA-BT-A20R TCGA-BT-A3PH TCGA-BT-A42B TCGA-DK-A1AD 
       27.62         2.50         5.06         4.67        17.56       112.44 
TCGA-DK-AA6X TCGA-E7-A4IJ TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3SO 
       15.35        22.16        12.95        14.37         8.09         5.52 
TCGA-FD-A5BV TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3I6 
        5.36        10.65         8.94         7.23        20.12        20.71 
TCGA-GC-A4ZW TCGA-GD-A6C6 TCGA-GU-A762 TCGA-K4-A5RJ TCGA-KQ-A41S TCGA-LC-A66R 
        0.49         2.20         7.63        17.72         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78M 
       15.58        13.48        12.23        16.67        38.99        22.68 
TCGA-UY-A8OD TCGA-XF-A9SG TCGA-XF-AAMG TCGA-ZF-AA5H TCGA-GU-AATO 
      112.83        48.62       110.60        29.49        10.65 

$`19Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42C TCGA-CF-A9FL 
       26.14        14.89         8.35        25.94        28.70        18.58 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
        4.90        15.12        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IU 
       16.70       130.88        46.68        87.32        50.27        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        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-AA6R 
       15.68        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
      166.03        13.64        13.64        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.35        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       60.66        24.30        23.41        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       19.79        12.85        27.35         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA 
       53.88        10.78         5.69        18.08         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       18.81         6.15        12.69         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC 
       31.07        17.23        17.62        70.32        21.40        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        3.45         2.76         9.14        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       46.98        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       97.45       125.49        97.12        15.35         3.22        15.98 
TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       14.93        12.76        21.04        26.27        18.90         2.24 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        10.82        11.31        54.90        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        3.88         9.63        13.64        21.11        94.29         3.48 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       34.06        19.69        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
       94.88       104.65        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        17.42        40.08         7.33         2.66         6.74 
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-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42E 
       14.96         5.06         8.25        17.16        16.18        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-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.34        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE 
       29.79         1.84        21.86        66.41        18.41        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
       13.58         8.15        20.81        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       13.58        18.81        19.00        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       29.72         5.36         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-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.07        15.32        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       22.52        27.98        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
       19.33        27.45         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.85        12.66         3.25        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
       26.93        59.31        66.02         6.94        29.36        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         8.94        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 
        3.12        20.98        11.31        18.97        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       21.24         9.07        11.70         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L 
       11.80        44.38        21.07        16.54        17.62        37.05 
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        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       17.82         6.21         3.85        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       17.88        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       28.24        16.27        92.98         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
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-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       19.40         8.52        54.21         5.52 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.49               0.56 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            112.83             166.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            14.370             17.965 
[1] "0.5 - 112.8 (14.4)" "0.6 - 166.0 (18.0)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         0       17        23       19
  19Q LOSS WILD-TYPE       2      112       117      116
D76V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                17                112
  STAGE III               23                117
  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   9
  19Q LOSS WILD-TYPE      111 163  49
D76V4, multiclass
          clus
vv         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1+T2               12                111
  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
  19Q LOSS MUTATED    30   6  11   2
  19Q LOSS WILD-TYPE 206  41  64   6
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               30                206
  N1                6                 41
  N2               11                 64
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    21   2
  19Q LOSS WILD-TYPE 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    16  43
  19Q LOSS WILD-TYPE  91 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     16   43
  19Q LOSS WILD-TYPE   91  258
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               16                 91
  MALE                 43                258
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    54   1
  19Q LOSS WILD-TYPE 310  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     54    1
  19Q LOSS WILD-TYPE  310   19
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                54                310
  YES                1                 19
[1] 2 2
[1] FALSE
D76V9, continuous
D76V10, continuous
D76V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       4                         2    51
  19Q LOSS WILD-TYPE    39                        20   276
D76V12, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    4                 39
  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"
D76V13, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2  53
  19Q LOSS WILD-TYPE   7 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   53
  19Q LOSS WILD-TYPE    7  316
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               53                316
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    15  17
  20P LOSS WILD-TYPE 212 161
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                32                373 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                17                161 
$`20P LOSS MUTATED`
TCGA-BT-A20N TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-FD-A5C0 TCGA-FD-A6TB TCGA-G2-A3VY 
       26.14        66.05        64.18        18.08        18.81        17.62 
TCGA-G2-AA3D TCGA-GV-A3JZ TCGA-K4-A4AC TCGA-UY-A78N TCGA-XF-A8HE TCGA-XF-A9SW 
       70.32        19.82         9.14        86.83       125.49        11.90 
TCGA-XF-AAML TCGA-XF-AAN7 TCGA-4Z-AA7W TCGA-BT-A20J TCGA-BT-A20P TCGA-CF-A47S 
        7.63        18.58        27.62        19.04        17.88        10.95 
TCGA-CF-A5U8 TCGA-CF-A8HY TCGA-DK-A1A3 TCGA-DK-A3IM TCGA-E7-A6MD TCGA-E7-A85H 
       13.12        11.34        21.86         8.15         4.24        12.95 
TCGA-GU-A42R TCGA-GU-AATQ TCGA-HQ-A2OE TCGA-UY-A78K TCGA-XF-AAMX TCGA-ZF-A9R9 
       18.97         7.00        38.60        17.62         6.77        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF 
       13.41        64.08 

$`20P LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
        9.67        17.98        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       12.85        27.35         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       10.78         5.69         8.25        58.92         6.28        62.86 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3RB 
       31.07        17.23        11.08        33.01        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF 
       17.75        24.92        10.92        32.78        32.98        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        3.45         2.76        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD 
       46.98        14.24         1.84        33.14        51.32        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        12.76        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       86.30         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        17.16        34.98        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       17.42        40.08         7.33         2.66         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       13.15        12.16        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        8.25        17.16        16.18         4.67        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-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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 
       11.87        13.08         5.19        29.79         1.84        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX 
        7.79       142.78         4.80        13.58        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
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         5.36        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-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       24.03        24.66        13.68        14.07        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.91        14.07         0.49         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
        2.10         3.12        20.98         2.20        11.31         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       20.05        15.78         4.73        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE 
        8.48        36.49         1.51        19.40        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       21.24         9.07        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       21.07        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        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        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       45.04         6.58         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       79.66        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 
       92.98       110.60         2.96         8.32        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       75.39        18.84         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       31.20        35.84        21.86        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89         8.61        59.38        60.16        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              4.24               0.49 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            125.49             166.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             18.33              17.42 
[1] "4.2 - 125.5 (18.3)" "0.5 - 166.0 (17.4)"
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         0       10         9       12
  20P LOSS WILD-TYPE       2      119       131      123
D77V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                10                119
  STAGE III                9                131
  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
  20P LOSS MUTATED         11  16   3
  20P LOSS WILD-TYPE      112 179  55
D77V4, multiclass
          clus
vv         20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1+T2               11                112
  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
  20P LOSS MUTATED    17   3   9   1
  20P LOSS WILD-TYPE 219  44  66   7
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               17                219
  N1                3                 44
  N2                9                 66
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    13   0
  20P LOSS WILD-TYPE 179  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     13    0
  20P LOSS WILD-TYPE  179   11
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               13                179
  1                0                 11
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     5  27
  20P LOSS WILD-TYPE 102 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5   27
  20P LOSS WILD-TYPE  102  274
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                5                102
  MALE                 27                274
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    26   2
  20P LOSS WILD-TYPE 338  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     26    2
  20P LOSS WILD-TYPE  338   18
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                26                338
  YES                2                 18
[1] 2 2
[1] FALSE
D77V9, continuous
D77V10, continuous
D77V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       6                         1    23
  20P LOSS WILD-TYPE    37                        21   304
D77V12, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    6                 37
  BLACK OR AFRICAN AMERICAN                1                 21
  WHITE                                   23                304
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  29
  20P LOSS WILD-TYPE   9 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   29
  20P LOSS WILD-TYPE    9  340
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  9
  NOT HISPANIC OR LATINO               29                340
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     6   9
  20Q LOSS WILD-TYPE 221 169
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                15                390 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                169 
$`20Q LOSS MUTATED`
TCGA-DK-A2I6 TCGA-GV-A3JZ TCGA-UY-A78N TCGA-XF-A9SW TCGA-XF-AAML TCGA-XF-AAN7 
       87.32        19.82        86.83        11.90         7.63        18.58 
TCGA-4Z-AA7W TCGA-BT-A20P TCGA-CF-A8HY TCGA-DK-A1A3 TCGA-E7-A6MD TCGA-GU-AATQ 
       27.62        17.88        11.34        21.86         4.24         7.00 
TCGA-HQ-A5NE TCGA-XF-AAMW TCGA-ZF-A9RF 
       12.16         8.32        64.08 

$`20Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       28.70         8.98        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       46.68         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y 
       46.78        19.79        12.85        27.35         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.36         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF 
       17.75        24.92        10.92        32.78        32.98        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH 
       35.97        46.98        14.24         1.84        33.14        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       97.45       125.49        97.12        15.35         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 
       34.45        14.93         4.21        12.76        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       11.31        54.90        71.57        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       30.94        61.45        86.30         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       21.11        30.28        94.29         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         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-A20Q 
        6.74         6.58        13.15        19.04        12.16        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        17.56        36.43        28.41         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-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 
       13.08         5.19        29.79         1.84        66.41        18.41 
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-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
      142.78         4.80        13.58         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
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         5.36        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-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       24.03        24.66        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-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       20.91        19.33         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
        7.23        20.12        66.02         6.94        29.36        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-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV 
       18.97         7.63        20.05        15.78         4.73        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       38.60        64.01        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.32        15.58        21.07        13.48        12.23        16.67 
TCGA-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-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       78.25        69.34         3.02       112.83        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       17.82         6.21         3.85        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
       23.64        28.24        16.27        92.98       110.60         2.96 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        6.77        56.48        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       28.41        13.41        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              4.24               0.49 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             87.32             166.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             17.88              17.62 
[1] "4.2 - 87.3 (17.9)"  "0.5 - 166.0 (17.6)"
[1] "hr=" "1.5"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         0        4         3        8
  20Q LOSS WILD-TYPE       2      125       137      127
D78V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                 4                125
  STAGE III                3                137
  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   6   2
  20Q LOSS WILD-TYPE      116 189  56
D78V4, multiclass
          clus
vv         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1+T2                7                116
  T3                      6                189
  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     7   4   2   1
  20Q LOSS WILD-TYPE 229  43  73   7
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                7                229
  N1                4                 43
  N2                2                 73
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     8   0
  20Q LOSS WILD-TYPE 184  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      8    0
  20Q LOSS WILD-TYPE  184   11
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                8                184
  1                0                 11
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2  13
  20Q LOSS WILD-TYPE 105 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2   13
  20Q LOSS WILD-TYPE  105  288
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                105
  MALE                 13                288
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    13   0
  20Q LOSS WILD-TYPE 351  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     13    0
  20Q LOSS WILD-TYPE  351   20
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                13                351
  YES                0                 20
[1] 2 2
[1] FALSE
D78V9, continuous
D78V10, continuous
D78V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       1                         0    13
  20Q LOSS WILD-TYPE    42                        22   314
D78V12, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    1                 42
  BLACK OR AFRICAN AMERICAN                0                 22
  WHITE                                   13                314
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    41  38
  21Q LOSS WILD-TYPE 186 140
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                79                326 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                38                140 
$`21Q LOSS MUTATED`
TCGA-BT-A20T TCGA-CU-A0YN TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A6B6 TCGA-DK-AA6R 
       14.89        12.92         8.22        17.72        36.66       165.73 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-FD-A3SL TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BY 
       13.64        13.64        23.41         3.62        15.58         8.25 
TCGA-FD-A6TA TCGA-FD-A6TD TCGA-G2-AA3D TCGA-GC-A3YS TCGA-GV-A6ZA TCGA-HQ-A5ND 
       62.86        12.69        70.32        24.92        22.72         9.01 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41O TCGA-XF-A8HG TCGA-XF-A9T5 TCGA-XF-A9T8 
        2.76         9.14        50.56        15.35        66.64        13.74 
TCGA-XF-AAML TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-2F-A9KO 
        7.63        61.45        18.58        34.06        57.90        24.13 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BT-A20V TCGA-BT-A20X 
        0.62        51.16        10.22        47.80         5.06         8.25 
TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-AA6Q 
       36.43        12.79        12.62         5.19         1.84        13.58 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A6MD TCGA-FD-A3B5 TCGA-FD-A3SO 
       15.35        12.03        43.59         4.24         8.94         5.52 
TCGA-FD-A5BV TCGA-FD-A6TF TCGA-FD-A6TK TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-AA3F 
        5.36         2.27        10.85        61.94        48.00        29.36 
TCGA-GC-A6I1 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3QI TCGA-HQ-A2OF TCGA-K4-A5RI 
        8.94         4.73        14.27        36.49        64.01        11.70 
TCGA-K4-A5RJ TCGA-LT-A5Z6 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD 
       17.72        15.58        76.01        78.25        69.34       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-AAMG TCGA-ZF-A9R0 
       35.24        29.56        79.66        23.64       110.60        22.36 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA56 
       21.86        13.41        20.22         2.89        60.16         8.52 
TCGA-ZF-AA5H 
       29.49 

$`21Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       26.14         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
        8.98        18.58         4.90        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
        2.14        19.00        16.70       130.88        46.68        87.32 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        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-AA6S TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
       38.24        52.01       166.03        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.35        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       60.66        24.30        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       12.85        27.35        26.73        53.88        10.78         5.69 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
       18.08        58.92         6.28        18.81         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P 
       33.01        17.62        21.40        19.13        17.75        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41P 
       19.07        25.02         3.45        27.68        52.73        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       46.98        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       97.45       125.49        97.12         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       18.90         2.24         2.10        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 
       71.57        91.73        98.99        44.32        30.94        86.30 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
        3.88         9.63        13.64        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ 
        3.48        88.87        19.69        12.23        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM 
       27.62        50.04        41.75        66.54         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         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-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 
       17.16        16.18         4.67        17.56        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       23.01        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-A47Y 
       12.16        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-A9FM TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       13.08        29.79        21.86        66.41        18.41       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-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.02        18.81        19.00        38.83        29.72         5.36 
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-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       26.24        24.03        24.66        13.68        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-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       22.52        27.98        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FJ-A3Z9 
       19.33        27.45         2.70         7.10        13.35        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       10.65         8.94         3.25        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.23        20.12        66.02         6.94        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         0.49        13.91        26.70         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-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       20.05        15.78         7.00        21.34        19.10         8.48 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
        1.51        19.40        38.60        12.16        21.24         9.07 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        15.42        16.27        11.80        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        21.07        13.48        12.23        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PD 
       38.99        17.62        37.05        22.68         3.02        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI 
        6.21         3.85        45.04         6.58         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 
       48.62        64.80        66.41         5.98        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
       92.98         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39        18.84         0.66        11.97        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4U 
       35.84        28.41        64.08        58.72        47.84         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 
       59.38        67.20        56.35        35.41        19.40        54.21 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.62               0.49 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            165.73             166.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            15.580             17.685 
[1] "0.6 - 165.7 (15.6)" "0.5 - 166.0 (17.7)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         0       24        25       30
  21Q LOSS WILD-TYPE       2      105       115      105
D79V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                24                105
  STAGE III               25                115
  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
  21Q LOSS MUTATED         20  39  12
  21Q LOSS WILD-TYPE      103 156  46
D79V4, multiclass
          clus
vv         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1+T2               20                103
  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    42  20  10   0
  21Q LOSS WILD-TYPE 194  27  65   8
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               42                194
  N1               20                 27
  N2               10                 65
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    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  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     73    3
  21Q LOSS WILD-TYPE  291   17
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                73                291
  YES                3                 17
[1] 2 2
[1] FALSE
D79V9, continuous
D79V10, continuous
D79V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       3                         6    67
  21Q LOSS WILD-TYPE    40                        16   260
D79V12, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    3                 40
  BLACK OR AFRICAN AMERICAN                6                 16
  WHITE                                   67                260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2  70
  21Q LOSS WILD-TYPE   7 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   70
  21Q LOSS WILD-TYPE    7  299
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  7
  NOT HISPANIC OR LATINO               70                299
[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 139 107
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               159                246 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                71                107 
$`22Q LOSS MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A3KJ 
       16.27        16.77        28.70         8.98        12.92        18.48 
TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 
       46.68         8.22        17.72        21.30         9.67        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       67.36        15.68        50.70        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3SJ 
       13.64        11.18        15.35         1.22        33.04        24.30 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A5C0 
       29.16        19.79        12.85        15.58         8.25        18.08 
TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 
        6.28        18.81         6.15        12.69        12.36        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GU-AATP TCGA-GV-A40G 
       17.23        11.08        17.62        24.92        32.98        19.07 
TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-UY-A78N TCGA-XF-A8HF TCGA-XF-A8HG 
       22.72        25.02         3.45        86.83        97.12        15.35 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY 
        3.22        15.98        34.45         4.21        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 
       26.27         2.24        10.82        44.32        61.45        86.30 
TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-4Z-AA7W 
       13.64        94.29         3.48        34.06        19.69        27.62 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BT-A20J 
        0.62        41.75        10.22        47.80         2.66        19.04 
TCGA-BT-A20R TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A3MI 
        5.06        17.56        36.43         1.94        23.01        12.16 
TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       12.62         5.19        18.41        17.95         7.79       142.78 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58         8.15        13.58        15.35        12.03        43.59 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7PW TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        0.56        24.03        13.68        32.02        16.77         8.94 
TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.52         5.52        22.98        20.91         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A6TF TCGA-FD-A6TK TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3RC 
        2.70         2.27        10.85         7.23        20.12        15.91 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
        0.49         8.94        13.91        26.70         2.10         2.20 
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        15.78        19.10 
TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       19.40        12.16         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.42         1.15        15.32        13.48        12.23        16.67 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB 
       38.99        17.62        37.05        69.34        35.24        29.56 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A9SG TCGA-XF-A9SX 
        6.21         3.85        45.04         6.58        48.62        23.64 
TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9R7 
       28.24       110.60         2.96        56.48        11.97        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4X 
       28.41        13.41        47.84        20.22         8.61        67.20 
TCGA-ZF-AA52 TCGA-ZF-AA5H TCGA-GU-AATO 
       35.41        29.49        10.65 

$`22Q LOSS WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        15.12        33.83        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO 
        8.35        20.48        25.94         9.96        18.58         4.90 
TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       15.12        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
       87.32        50.27        23.21        66.05        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       76.60        36.66        38.24        13.64        56.15        20.32 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
       25.58         0.92         4.01        60.66        23.41        17.98 
TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       46.78        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        5.69        58.92        62.86         3.06         4.31         9.67 
TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P 
       33.01        70.32        21.40        19.13        17.75        10.92 
TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A5ND 
       32.78        19.82        20.28        27.35         8.58         9.01 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD 
       46.98        14.24         1.84        33.14        51.32        97.45 
TCGA-XF-A8HE TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 
      125.49        14.93        12.76        18.90        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 
       98.99        30.94        18.58         3.88         9.63        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       30.28        88.87        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM 
       34.98        50.04        51.16        66.54         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
       40.08         7.33         6.74         6.58        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       17.88        19.50        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       16.18         4.67        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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.34        11.87        13.08        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK 
       66.41       112.44        16.14        17.62        15.62         4.80 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
       20.81        10.55       163.30        15.02        18.81        19.00 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        22.16         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN 
        0.66        26.96        26.24         4.24        24.66        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B8 TCGA-FD-A3N6 
       12.95        15.32        14.37         8.09        12.62        27.98 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62O TCGA-FD-A62S TCGA-FJ-A3Z9 
       25.74        14.96        19.33         7.10        13.35        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-A2EO TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
       26.93        59.31        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A767 TCGA-GU-AATQ 
       15.81        14.07         3.12        20.98         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE 
       14.27        21.34         8.48        36.49         1.51        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A5Z6 
       64.01        21.24        16.27        11.80        44.38        15.58 
TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       21.07        16.54        22.68        76.01        78.25         3.02 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
      112.83        17.82         1.87        17.88        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAMX 
       66.41         5.98        16.27        92.98         8.32         6.77 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4V 
       31.20        35.84        64.08        58.72         2.89        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       60.16        56.35        19.40         8.52        54.21         5.52 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.49               0.66 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            166.03             163.30 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             16.77              17.93 
[1] "0.5 - 166.0 (16.8)" "0.7 - 163.3 (17.9)"
[1] "hr=" "1.2"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         0       41        54       65
  22Q LOSS WILD-TYPE       2       88        86       70
D80V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  0                  2
  STAGE II                41                 88
  STAGE III               54                 86
  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  81  27
  22Q LOSS WILD-TYPE       84 114  31
D80V4, multiclass
          clus
vv         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1+T2               39                 84
  T3                     81                114
  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    80  20  41   3
  22Q LOSS WILD-TYPE 156  27  34   5
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               80                156
  N1               20                 27
  N2               41                 34
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    57   3
  22Q LOSS WILD-TYPE 135   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     57    3
  22Q LOSS WILD-TYPE  135    8
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               57                135
  1                3                  8
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    42 118
  22Q LOSS WILD-TYPE  65 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     42  118
  22Q LOSS WILD-TYPE   65  183
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               42                 65
  MALE                118                183
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   142   5
  22Q LOSS WILD-TYPE 222  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    142    5
  22Q LOSS WILD-TYPE  222   15
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               142                222
  YES                5                 15
[1] 2 2
[1] FALSE
D80V9, continuous
D80V10, continuous
D80V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       8                         8   136
  22Q LOSS WILD-TYPE    35                        14   191
D80V12, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    8                 35
  BLACK OR AFRICAN AMERICAN                8                 14
  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"
D80V13, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     7 141
  22Q LOSS WILD-TYPE   2 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7  141
  22Q LOSS WILD-TYPE    2  228
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  2
  NOT HISPANIC OR LATINO              141                228
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    40  33
  XP LOSS WILD-TYPE 187 145
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               73               332 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               33               145 
$`XP LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA84 TCGA-BT-A20T TCGA-CU-A0YN TCGA-DK-A1A5 TCGA-DK-A1AB 
      108.95        15.12        14.89        12.92         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-AA6W TCGA-DK-AA71 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3SN TCGA-FD-A3SR 
       13.64        13.64         0.92        33.04        29.16        19.79 
TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A6TC TCGA-G2-A3VY TCGA-GV-A40G 
       12.85        15.58         8.25         6.15        17.62        19.07 
TCGA-HQ-A5ND TCGA-KQ-A41O TCGA-S5-A6DX TCGA-XF-A8HF TCGA-XF-A9SM TCGA-XF-A9SP 
        9.01        50.56         1.84        97.12        34.45        14.93 
TCGA-XF-AAML TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O 
        7.63        88.87        34.06       104.65         8.35        16.83 
TCGA-5N-A9KI TCGA-BT-A3PH TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH 
        2.50         4.67        17.56        13.97        12.13        13.08 
TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CU-A3QU TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 
       12.62        12.10         5.19        13.58        18.81        12.03 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-FD-A3B4 TCGA-FD-A62N TCGA-FD-A6TF TCGA-G2-A2EL 
       43.59        29.72        16.77         2.70         2.27        26.93 
TCGA-G2-A3IB TCGA-G2-AA3F TCGA-GC-A4ZW TCGA-GU-A42R TCGA-GV-A3JX TCGA-HQ-A2OF 
        7.23        29.36         0.49        18.97        19.10        64.01 
TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       21.24        17.72         1.81        11.80        15.58        12.23 
TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A8OD TCGA-XF-A9SZ TCGA-XF-AAMT TCGA-ZF-A9R9 
       16.54        78.25       112.83        28.24         2.96        28.41 
TCGA-ZF-AA4U 
        8.61 

$`XP LOSS WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W 
       16.27        16.77        33.83        12.39        26.14         8.35 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL 
       20.48        25.94         9.96        28.70         8.98        18.58 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AC 
        4.90        15.12        18.48        13.58        19.00       130.88 
TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 
       46.68         8.22        17.72        23.21        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       64.18        53.29        76.60        67.36        15.68        36.66 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
       52.01       165.73       166.03        56.15        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       15.35        25.58         1.22         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       23.41        17.98        46.78        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       53.88        10.78         5.69        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       62.86        18.81        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D 
        9.67        31.07        17.23        11.08        33.01        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
       32.98        19.82        20.28        27.35         8.58        22.72 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       35.97        46.98        14.24        33.14        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST 
       97.45       125.49        15.35         3.22        15.98         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
       30.28        94.29         3.48        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S 
       24.13        11.97        94.88        44.94        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-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        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-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       16.18        36.43        28.41         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.56        12.59        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A8HY 
       12.10        12.26        13.12        12.00        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       11.87        13.08        29.79         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
        7.79       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A4U1 
       10.55       163.30        15.02        19.00        15.35        38.83 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        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-A7PW 
       26.96        26.24         4.24        24.03        24.66        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-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        7.10        13.35        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IE 
        3.25        61.94        48.00        15.95        59.31        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       66.02         6.94        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
        2.20        11.31         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
        7.00        14.27        21.34         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB 
       19.40        38.60        12.16         9.07        11.70        15.42 
TCGA-K4-A83P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V 
       16.27        44.38         1.15        15.32        21.07        13.48 
TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.67        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       69.34         3.02        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        3.85        45.04         6.58         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 
       64.80        79.66        66.41         5.98        23.64        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
       92.98       110.60         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       75.39        18.84         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       31.20        35.84        21.86        13.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       47.84        20.22         2.89        59.38        60.16        67.20 
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        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.49              0.56 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           112.83            166.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           15.580            17.965 
[1] "0.5 - 112.8 (15.6)" "0.6 - 166.0 (18.0)"
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP LOSS MUTATED         0       27        23       23
  XP LOSS WILD-TYPE       2      102       117      112
D81V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               27               102
  STAGE III              23               117
  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 LOSS MUTATED         22  32  11
  XP LOSS WILD-TYPE      101 163  47
D81V4, multiclass
          clus
vv         XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1+T2              22               101
  T3                    32               163
  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
  XP LOSS MUTATED    42  11  11   1
  XP LOSS WILD-TYPE 194  36  64   7
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              42               194
  N1              11                36
  N2              11                64
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    32   2
  XP LOSS WILD-TYPE 160   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     32    2
  XP LOSS WILD-TYPE  160    9
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              32               160
  1               2                 9
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    17  56
  XP LOSS WILD-TYPE  90 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     17   56
  XP LOSS WILD-TYPE   90  245
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              17                90
  MALE                56               245
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    64   5
  XP LOSS WILD-TYPE 300  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     64    5
  XP LOSS WILD-TYPE  300   15
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               64               300
  YES               5                15
[1] 2 2
[1] FALSE
D81V9, continuous
D81V10, continuous
D81V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       7                         5    57
  XP LOSS WILD-TYPE    36                        17   270
D81V12, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   7                36
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                  57               270
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2  65
  XP LOSS WILD-TYPE   7 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   65
  XP LOSS WILD-TYPE    7  304
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 7
  NOT HISPANIC OR LATINO              65               304
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    49  34
  XQ LOSS WILD-TYPE 178 144
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               83               322 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               34               144 
$`XQ LOSS MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA84 TCGA-BT-A20T TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC 
      108.95        15.12        14.89         2.14        16.70       130.88 
TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6B5 TCGA-DK-AA6W 
       87.32        50.27        21.30         9.67        50.70        13.64 
TCGA-DK-AA71 TCGA-E7-A7DU TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A5BY 
       13.64         0.92        29.16        19.79        12.85         8.25 
TCGA-FJ-A3Z7 TCGA-GU-A42P TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A54R TCGA-KQ-A41O 
       31.07        10.92        19.07         9.01        27.68        50.56 
TCGA-S5-A6DX TCGA-XF-A8HF TCGA-XF-A9SP TCGA-XF-AAN7 TCGA-ZF-A9RL TCGA-ZF-AA4R 
        1.84        97.12        14.93        18.58        88.87        34.06 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA80 TCGA-BT-A2LB TCGA-BT-A3PH 
      104.65         8.35        16.83         0.62        16.18         4.67 
TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47X TCGA-CF-A7I0 
       17.56        13.97        12.13        13.08        12.62        12.10 
TCGA-CU-A3QU TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 
        5.19        13.58        18.81        12.03        43.59        29.72 
TCGA-FD-A3B4 TCGA-FD-A62N TCGA-FD-A6TF TCGA-FT-A3EE TCGA-G2-A2EL TCGA-G2-A3IB 
       16.77         2.70         2.27         3.25        26.93         7.23 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A4ZW TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GV-A3JX 
       66.02        29.36         0.49         2.20        18.97        19.10 
TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6FZ 
       36.49        38.60        64.01        21.24        17.72         1.81 
TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A8OD 
       11.80        15.58        12.23        16.54        78.25       112.83 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SZ TCGA-XF-AAMG 
       17.82         3.85         6.58        17.88        28.24       110.60 
TCGA-XF-AAMT TCGA-YF-AA3L TCGA-ZF-A9R9 TCGA-ZF-A9RM TCGA-ZF-AA4U 
        2.96        11.97        28.41        47.84         8.61 

$`XQ LOSS WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W 
       16.27        16.77        33.83        12.39        26.14         8.35 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL 
       20.48        25.94         9.96        28.70         8.98        18.58 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA 
       12.92         4.90        15.12        18.48        13.58        19.00 
TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 
       46.68         8.22        17.72        23.21        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       64.18        53.29        76.60        67.36        15.68        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA74 TCGA-DK-AA75 
       38.24        52.01       165.73       166.03        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       20.32        15.35        25.58         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A43P 
       60.66        24.30        23.41        17.98        46.78        27.35 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
        3.62        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       18.08        58.92         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF 
       12.69        12.36         3.06         4.31         9.67        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       11.08        33.01        17.62        70.32        21.40        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.75        24.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       27.35         8.58        22.72        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 
        9.14        52.73        35.97        46.98        14.24        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SJ 
       86.83        51.32        97.45       125.49        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       15.98        34.45         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 
       98.99        44.32        30.94        61.45        86.30         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        9.63        13.64        21.11        30.28        94.29         3.48 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
       19.69        57.90        12.23        24.13        11.97        94.88 
TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       44.94        17.16        34.98        27.62        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         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-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        5.06         8.25        17.16        36.43        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47S 
       23.01        12.79        12.56        12.59        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-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.34        11.87        13.08        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6U 
        8.15        20.81        10.55       163.30        15.02        19.00 
TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83         5.36        22.16         2.24        16.70 
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-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-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.09        32.02         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 
        5.36        27.45         7.10        13.35        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
       10.65         8.94        61.94        48.00        15.95        59.31 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12         6.94        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       11.31         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5NE 
       14.27        21.34         8.48         1.51        19.40        12.16 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R TCGA-KQ-A41S 
        9.07        11.70        15.42        16.27        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K 
       15.32        21.07        13.48        16.67        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       37.05        22.68        76.01        69.34         3.02        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH 
       29.56         6.21        45.04         1.87        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME 
       79.66        66.41         5.98        23.64        16.27        92.98 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
        8.32         6.77        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        0.66        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V 
       13.41        64.08        58.72        20.22         2.89        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.49              0.56 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           130.88            166.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           16.700            17.915 
[1] "0.5 - 130.9 (16.7)" "0.6 - 166.0 (17.9)"
[1] "hr=" "1.1"
D82V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         0       29        25       28
  XQ LOSS WILD-TYPE       2      100       115      107
D82V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 0                 2
  STAGE II               29               100
  STAGE III              25               115
  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
  XQ LOSS MUTATED         27  38  11
  XQ LOSS WILD-TYPE       96 157  47
D82V4, multiclass
          clus
vv         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1+T2              27                96
  T3                    38               157
  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
  XQ LOSS MUTATED    48  12  16   1
  XQ LOSS WILD-TYPE 188  35  59   7
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              48               188
  N1              12                35
  N2              16                59
  N3               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    36   2
  XQ LOSS WILD-TYPE 156   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     36    2
  XQ LOSS WILD-TYPE  156    9
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              36               156
  1               2                 9
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    20  63
  XQ LOSS WILD-TYPE  87 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     20   63
  XQ LOSS WILD-TYPE   87  238
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              20                87
  MALE                63               238
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    73   5
  XQ LOSS WILD-TYPE 291  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     73    5
  XQ LOSS WILD-TYPE  291   15
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               73               291
  YES               5                15
[1] 2 2
[1] FALSE
D82V9, continuous
D82V10, continuous
D82V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       7                         5    65
  XQ LOSS WILD-TYPE    36                        17   262
D82V12, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   7                36
  BLACK OR AFRICAN AMERICAN               5                17
  WHITE                                  65               262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V13, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4  70
  XQ LOSS WILD-TYPE   5 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4   70
  XQ LOSS WILD-TYPE    5  299
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 5
  NOT HISPANIC OR LATINO              70               299
[1] 2 2
[1] FALSE
