[1] "ofn"        "-oTCOAD-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/COAD-TP/22506513/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/22508740/transformed.cor.cli.txt"

nPatients in clinical file=458, in cluster file=451, common to both=449
[1] "Reduce the number of clustering variables from 82 to 81."
[1]  81 449
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               409 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               409 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               81               368 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               81               368 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               82               367 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               82               367 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               79               370 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               79               370 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               47               402 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               47               402 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               64               385 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               64               385 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               437 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               437 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               432 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               432 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               68               381 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               68               381 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               40               409 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               40               409 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               84               365 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               84               365 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               76               373 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               76               373 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              245               204 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              245               204 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              222               227 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              222               227 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              134               315 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              134               315 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              226               223 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              226               223 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               81               368 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               81               368 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               71               378 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               71               378 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                38                411 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                38                411 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                23                426 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                23                426 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                54                395 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                54                395 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                51                398 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                51                398 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                93                356 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                93                356 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                88                361 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                88                361 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               255                194 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               255                194 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                35                414 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                35                414 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                438 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                438 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               106                343 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               106                343 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               104                345 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               104                345 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                29                420 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                29                420 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                84                365 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                84                365 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                23                426 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                23                426 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                14                435 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                14                435 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                73                376 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                73                376 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                84                365 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                84                365 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               242                207 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               242                207 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               319                130 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               319                130 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                24                425 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                24                425 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                12                437 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                12                437 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               68               381 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               68               381 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               79               370 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               79               370 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               92               357 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               92               357 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               54               395 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               54               395 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6               443 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6               443 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7               442 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7               442 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               53               396 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               53               396 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               34               415 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               34               415 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              137               312 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              137               312 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              125               324 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              125               324 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               60               389 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               60               389 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               80               369 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               80               369 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               33               416 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               33               416 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               45               404 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               45               404 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               445 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               445 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              136               313 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              136               313 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               424 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               424 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               53               396 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               53               396 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               53               396 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               53               396 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                67                382 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                67                382 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                72                377 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                72                377 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                50                399 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                50                399 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                62                387 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                62                387 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                48                401 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                48                401 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                50                399 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                50                399 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                12                437 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                12                437 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               137                312 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               137                312 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               157                292 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               157                292 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                31                418 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                31                418 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                28                421 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                28                421 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               234                215 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               234                215 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                64                385 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                64                385 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               251                198 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               251                198 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               267                182 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               267                182 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                40                409 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                40                409 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                33                416 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                33                416 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                43                406 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                43                406 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                445 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                445 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               123                326 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               123                326 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               144                305 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               144                305 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               63               386 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               63               386 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               50               399 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               50               399 
[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] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "NUMBER_OF_LYMPH_NODES"               
[17] "RACE"                                
[18] "ETHNICITY"                           

Input Data has 18 rows and 449 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=88,	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=249,	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=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	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=16,	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=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'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 449 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"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES" "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=58, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 11  77 305  55 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 11  77 305  55 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 11  77 305  55 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 11  77 305  55 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
262 105  82 
[1] "table(vv)"
vv
 N0  N1  N2 
262 105  82 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
262 105  82 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
262 105  82 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=21, binary=FALSE, numeric=TRUE
RACE, nv=4, 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    30  10
  1P GAIN WILD-TYPE 305  91
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               396 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10                91 
$`1P GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3688 TCGA-AD-6888 TCGA-CK-5912 TCGA-5M-AATE 
       45.60        13.02        19.00        15.52        49.08        39.45 
TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 
       43.76        44.91        35.11        16.57        36.53        32.45 
TCGA-A6-6654 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3855 TCGA-AA-3973 
       23.87        54.02         2.01        15.02        32.05        13.05 
TCGA-AA-A01D TCGA-AA-A02E TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4682 TCGA-AZ-4684 
       10.98         2.96         0.20        17.85        22.36        65.00 
TCGA-CA-5255 TCGA-CA-6716 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6167 TCGA-D5-6535 
       12.36        12.20        15.02        14.04        14.99        15.12 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A28C TCGA-DM-A28K 
        7.53        10.13        12.43       119.70        81.37        98.24 
TCGA-DM-A28M TCGA-NH-A50T TCGA-QG-A5YV TCGA-RU-A8FL 
       95.18        18.18        42.77        38.70 

$`1P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       34.03         0.99        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       21.99        39.06        21.37        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01         1.94         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       79.69        17.85        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
        9.53        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 
       37.05        37.25        37.02        34.65        32.75        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
        6.97        14.01        50.04        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       16.08        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
       33.04         1.02        26.01        37.02        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.65        32.94         5.13        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.46        12.39        12.59        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       20.42        17.75        18.25        25.48        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       26.47       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        46.75        74.79        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        12.79        16.80        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        21.90        60.13        11.90        70.03 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              0.2               0.0 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           119.70            148.01 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           18.590            22.075 
[1] "0.2 - 119.7 (18.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1P GAIN MUTATED         6        0        2        11         1         0
  1P GAIN WILD-TYPE      68        1       27       121         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           1          1          5          5        6
  1P GAIN WILD-TYPE        19          7         54         36       39
                   vv
clus                STAGE IVA STAGE IVB
  1P GAIN MUTATED           2         0
  1P GAIN WILD-TYPE        15         2
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  6                68
  STAGE IA                 0                 1
  STAGE II                 2                27
  STAGE IIA               11               121
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                19
  STAGE IIIA               1                 7
  STAGE IIIB               5                54
  STAGE IIIC               5                36
  STAGE IV                 6                39
  STAGE IVA                2                15
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     1   5  31   3
  1P GAIN WILD-TYPE  10  72 274  52
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               1                10
  T2               5                72
  T3              31               274
  T4               3                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  1P GAIN MUTATED    22  10   8
  1P GAIN WILD-TYPE 240  95  74
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              22               240
  N1              10                95
  N2               8                74
[1] 3 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    25   8
  1P GAIN WILD-TYPE 303  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     25    8
  1P GAIN WILD-TYPE  303   56
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              25               303
  1               8                56
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    16  24
  1P GAIN WILD-TYPE 197 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     16   24
  1P GAIN WILD-TYPE  197  212
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              16               197
  MALE                24               212
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    32   1
  1P GAIN WILD-TYPE 338   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     32    1
  1P GAIN WILD-TYPE  338    8
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               32               338
  YES               1                 8
[1] 2 2
[1] FALSE
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    37   3
  1P GAIN WILD-TYPE 345  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     37    3
  1P GAIN WILD-TYPE  345   59
                               clus
vv                              1P GAIN MUTATED 1P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       37               345
  COLON MUCINOUS ADENOCARCINOMA               3                59
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    26   0   4   4
  1P GAIN WILD-TYPE 297   4  21  21
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              26               297
  R1               0                 4
  R2               4                21
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     2
  1P GAIN WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           7    22
  1P GAIN WILD-TYPE                        52   190
D1V12, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      7                52
  WHITE                                         22               190
[1] 4 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     1  30
  1P GAIN WILD-TYPE   3 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   30
  1P GAIN WILD-TYPE    3  239
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              30               239
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    55  24
  1Q GAIN WILD-TYPE 280  77
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               79               357 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               24                77 
$`1Q GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3688 TCGA-AA-3939 TCGA-AD-6888 
       45.60        24.16        13.02        19.00        12.99        15.52 
TCGA-CK-5912 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 
       49.08        39.45        43.76        43.76        44.91        35.11 
TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3488 
       16.57        36.53        32.45        24.69        23.87         5.03 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3679 
       13.94        78.08        54.02         2.01        47.05        15.02 
TCGA-AA-3696 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
        5.03        10.06        32.05        31.07        17.03        27.02 
TCGA-AA-3947 TCGA-AA-3973 TCGA-AA-3994 TCGA-AA-A01D TCGA-AA-A01R TCGA-AA-A01X 
       33.01        13.05        27.02        10.98        35.01        26.01 
TCGA-AA-A02E TCGA-AA-A02Y TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4682 
        2.96        39.98        14.50         0.20        17.85        22.36 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6716 TCGA-CM-4746 
       65.00        12.10        11.74        12.36        12.20        37.02 
TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
       25.02        22.98        15.02         5.03        15.02        14.04 
TCGA-CM-6167 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 
       14.99        25.48        15.12        17.85         7.53        10.13 
TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28K 
       12.43       119.70        92.75        81.37        35.97        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6855 TCGA-G4-6297 
       95.18         8.61        31.96        11.11        47.41        82.39 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6311 TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV 
       74.56        65.85        39.42        18.18         9.93        42.77 
TCGA-RU-A8FL 
       38.70 

$`1Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        14.53         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
        0.99        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       15.62         4.80        12.66         1.61         9.53        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       43.43        42.90        42.28        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       34.65        32.75        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        21.76        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       16.24        24.92        61.84        56.25         9.63         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 
       21.01        24.00        29.95        20.98        61.02         6.97 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       14.01        50.04        47.01        11.01         5.98        37.05 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       17.03         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       53.00        18.05        31.00         2.01        24.00        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       20.98        34.03         2.01        21.99        16.08        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02        27.02         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02         1.02        33.04         1.02        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.65        32.94         5.13        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
        6.77        29.56         5.23         3.19        12.69        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       20.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       22.03        30.08        32.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       12.00        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        43.27         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
       13.41        13.35        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6463 
       14.04        26.47       119.93        60.79       117.07        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       43.04        33.67        13.25         0.53        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
        8.35        67.30        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       74.79        10.98        19.33        19.33        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       16.80        29.46        32.98         8.42        31.30        21.90 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       60.13        11.90        70.03 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              0.2               0.0 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           119.70            148.01 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            24.16             21.99 
[1] "0.2 - 119.7 (24.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1Q GAIN MUTATED        10        0        5        18         2         0
  1Q GAIN WILD-TYPE      64        1       24       114         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           4          1         11          9       15
  1Q GAIN WILD-TYPE        16          7         48         32       30
                   vv
clus                STAGE IVA STAGE IVB
  1Q GAIN MUTATED           5         0
  1Q GAIN WILD-TYPE        12         2
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 10                64
  STAGE IA                 0                 1
  STAGE II                 5                24
  STAGE IIA               18               114
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                4                16
  STAGE IIIA               1                 7
  STAGE IIIB              11                48
  STAGE IIIC               9                32
  STAGE IV                15                30
  STAGE IVA                5                12
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q GAIN MUTATED     1  10  58  12
  1Q GAIN WILD-TYPE  10  67 247  43
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               1                10
  T2              10                67
  T3              58               247
  T4              12                43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  1Q GAIN MUTATED    39  22  20
  1Q GAIN WILD-TYPE 223  83  62
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              39               223
  N1              22                83
  N2              20                62
[1] 3 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    52  20
  1Q GAIN WILD-TYPE 276  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     52   20
  1Q GAIN WILD-TYPE  276   44
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              52               276
  1              20                44
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    31  50
  1Q GAIN WILD-TYPE 182 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     31   50
  1Q GAIN WILD-TYPE  182  186
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              31               182
  MALE                50               186
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    67   2
  1Q GAIN WILD-TYPE 303   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     67    2
  1Q GAIN WILD-TYPE  303    7
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               67               303
  YES               2                 7
[1] 2 2
[1] FALSE
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    74   7
  1Q GAIN WILD-TYPE 308  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     74    7
  1Q GAIN WILD-TYPE  308   55
                               clus
vv                              1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       74               308
  COLON MUCINOUS ADENOCARCINOMA               7                55
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    56   0   8   5
  1Q GAIN WILD-TYPE 267   4  17  20
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              56               267
  R1               0                 4
  R2               8                17
  RX               5                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     2
  1Q GAIN WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          11    42
  1Q GAIN WILD-TYPE                        48   170
D2V12, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     11                48
  WHITE                                         42               170
[1] 4 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     1  54
  1Q GAIN WILD-TYPE   3 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   54
  1Q GAIN WILD-TYPE    3  215
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              54               215
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    59  19
  2P GAIN WILD-TYPE 276  82
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               78               358 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               19                82 
$`2P GAIN MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3562 TCGA-AA-3867 
       14.53        24.16         1.02        34.03        19.99        24.03 
TCGA-AA-A00L TCGA-AD-6548 TCGA-AD-6888 TCGA-G4-6310 TCGA-G4-6628 TCGA-NH-A8F7 
       38.04        21.37        15.52        63.62        79.69        17.85 
TCGA-3L-AA1B TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3807 
       15.62         1.61        39.45        43.76        37.02        34.65 
TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6652 TCGA-A6-6654 
       36.53        30.44        32.71        29.16        24.69        23.87 
TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 
        9.07        29.00        29.00        50.04        15.02        37.05 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3851 TCGA-AA-3971 TCGA-AA-A01I TCGA-AA-A01S 
       10.06        35.05        33.07        16.08        31.00         1.02 
TCGA-AA-A01X TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 
       26.01         5.79        22.42        27.42        16.44        16.31 
TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 
        0.20        18.84         5.13         3.19        12.59        12.20 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 
       10.06        85.45        21.99         8.02        29.06         5.03 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-D5-5537 
       17.03        15.02        14.04        29.03        21.99        45.40 
TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A1DA 
       55.92         4.80        17.13        14.30        13.41         7.50 
TCGA-DM-A280 TCGA-DM-A28F TCGA-F4-6459 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6627 
        7.76        35.97         8.61         8.35        74.56        74.79 
TCGA-NH-A50T TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL TCGA-SS-A7HO 
       18.18        12.79        29.46        32.98        38.70        60.13 

$`2P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        13.94        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03         8.05        19.07         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 
       24.00        19.07        21.99        39.06        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        23.51        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
       91.79         4.80        12.66         9.53        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        32.75        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       21.76        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 
        1.02        38.99         1.02        19.07         0.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        2.01        14.01        47.05        47.01        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        5.03        26.99         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
        2.01        21.99        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       35.01        33.04         1.02        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       26.47         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 
      109.28        58.39         1.41         5.65        32.94        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23        11.74        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.39        12.59        12.76        14.30        17.56       148.01 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        15.62        51.32        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 
       15.02        15.02        15.02        12.00        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       54.61        19.59        56.09        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       18.25        25.48        43.27        15.12        17.85        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      135.65       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24        95.18        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31       133.18        82.39        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V 
       26.43        26.04        13.78        46.75        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 
       19.33         9.93        15.65        16.80        42.77         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        11.90        70.03 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              0.2               0.0 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            85.45            148.01 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           21.990            22.075 
[1] "0.2 - 85.5 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2P GAIN MUTATED        10        0        5        21         1         1
  2P GAIN WILD-TYPE      64        1       24       111         9         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           5          2         14          8        8
  2P GAIN WILD-TYPE        15          6         45         33       37
                   vv
clus                STAGE IVA STAGE IVB
  2P GAIN MUTATED           4         1
  2P GAIN WILD-TYPE        13         1
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 10                64
  STAGE IA                 0                 1
  STAGE II                 5                24
  STAGE IIA               21               111
  STAGE IIB                1                 9
  STAGE IIC                1                 0
  STAGE III                5                15
  STAGE IIIA               2                 6
  STAGE IIIB              14                45
  STAGE IIIC               8                33
  STAGE IV                 8                37
  STAGE IVA                4                13
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED     2  11  62   7
  2P GAIN WILD-TYPE   9  66 243  48
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               2                 9
  T2              11                66
  T3              62               243
  T4               7                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  2P GAIN MUTATED    41  21  20
  2P GAIN WILD-TYPE 221  84  62
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              41               221
  N1              21                84
  N2              20                62
[1] 3 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    54  13
  2P GAIN WILD-TYPE 274  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     54   13
  2P GAIN WILD-TYPE  274   51
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              54               274
  1              13                51
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    37  45
  2P GAIN WILD-TYPE 176 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     37   45
  2P GAIN WILD-TYPE  176  191
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              37               176
  MALE                45               191
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    69   2
  2P GAIN WILD-TYPE 301   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     69    2
  2P GAIN WILD-TYPE  301    7
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               69               301
  YES               2                 7
[1] 2 2
[1] FALSE
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    75   7
  2P GAIN WILD-TYPE 307  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     75    7
  2P GAIN WILD-TYPE  307   55
                               clus
vv                              2P GAIN MUTATED 2P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       75               307
  COLON MUCINOUS ADENOCARCINOMA               7                55
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    56   2   3   7
  2P GAIN WILD-TYPE 267   2  22  18
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              56               267
  R1               2                 2
  R2               3                22
  RX               7                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     3
  2P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          15    43
  2P GAIN WILD-TYPE                        44   169
D3V12, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                     15                44
  WHITE                                         43               169
[1] 4 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     2  56
  2P GAIN WILD-TYPE   2 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   56
  2P GAIN WILD-TYPE    2  213
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              56               213
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    56  19
  2Q GAIN WILD-TYPE 279  82
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               75               361 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19                82 
$`2Q GAIN MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3562 TCGA-AA-3867 
       14.53        24.16         1.02        34.03        19.99        24.03 
TCGA-AD-6548 TCGA-AD-6888 TCGA-G4-6310 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       21.37        15.52        63.62        79.69        17.85        15.62 
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 
        1.61        39.45        43.76        34.65        36.53        30.44 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3519 TCGA-AA-3532 
       32.71        29.16        24.69        23.87         9.07        29.00 
TCGA-AA-3534 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       29.00        50.04        15.02        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3851 TCGA-AA-3971 TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X 
       35.05        33.07        16.08        31.00         1.02        26.01 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK 
        5.79        22.42        27.42        16.44        16.31        18.84 
TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4950 TCGA-CK-5914 
        5.13         3.19        12.59        12.20        85.45        21.99 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
        8.02        29.06         5.03        15.02        14.04        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6538 
       21.99        14.99        45.40        55.92         4.80        17.13 
TCGA-DM-A1DA TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28F TCGA-F4-6459 TCGA-G4-6295 
        7.50         7.76        14.04        35.97         8.61         8.35 
TCGA-G4-6299 TCGA-G4-6311 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GC TCGA-QG-A5YW 
       74.56        39.42        74.79        18.18        12.79        29.46 
TCGA-QG-A5YX TCGA-RU-A8FL TCGA-SS-A7HO 
       32.98        38.70        60.13 

$`2Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        13.94        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03         8.05        19.07         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6895 
       24.00        19.07        38.04        21.99        39.06        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 
       26.17        91.79         4.80        12.66         9.53        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 
       16.57        37.05        37.25        37.02        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.06        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        20.61        21.76        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
        0.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       11.01         5.98        26.99         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        21.99        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01        33.04         1.02        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       24.53        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.85        19.33       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
        6.77        12.10        29.56         5.23        11.74        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.46        12.39        12.59        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56       148.01        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
       37.02        25.02        26.04        27.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       17.03        12.00        16.04        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        54.61        19.59        56.09 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12        17.85        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       82.39        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       85.48        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       46.75        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       16.80        42.77         8.42        31.30        21.90        11.90 
TCGA-WS-AB45 
       70.03 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.02              0.00 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            85.45            148.01 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            21.99             22.06 
[1] "1.0 - 85.5 (22.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2Q GAIN MUTATED        10        0        5        17         1         1
  2Q GAIN WILD-TYPE      64        1       24       115         9         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           6          2         14          9        8
  2Q GAIN WILD-TYPE        14          6         45         32       37
                   vv
clus                STAGE IVA STAGE IVB
  2Q GAIN MUTATED           3         1
  2Q GAIN WILD-TYPE        14         1
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 10                64
  STAGE IA                 0                 1
  STAGE II                 5                24
  STAGE IIA               17               115
  STAGE IIB                1                 9
  STAGE IIC                1                 0
  STAGE III                6                14
  STAGE IIIA               2                 6
  STAGE IIIB              14                45
  STAGE IIIC               9                32
  STAGE IV                 8                37
  STAGE IVA                3                14
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED     2  11  60   6
  2Q GAIN WILD-TYPE   9  66 245  49
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               2                 9
  T2              11                66
  T3              60               245
  T4               6                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  2Q GAIN MUTATED    37  21  21
  2Q GAIN WILD-TYPE 225  84  61
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              37               225
  N1              21                84
  N2              21                61
[1] 3 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    52  12
  2Q GAIN WILD-TYPE 276  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     52   12
  2Q GAIN WILD-TYPE  276   52
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              52               276
  1              12                52
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    36  43
  2Q GAIN WILD-TYPE 177 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     36   43
  2Q GAIN WILD-TYPE  177  193
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              36               177
  MALE                43               193
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    66   2
  2Q GAIN WILD-TYPE 304   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     66    2
  2Q GAIN WILD-TYPE  304    7
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               66               304
  YES               2                 7
[1] 2 2
[1] FALSE
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    72   7
  2Q GAIN WILD-TYPE 310  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     72    7
  2Q GAIN WILD-TYPE  310   55
                               clus
vv                              2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       72               310
  COLON MUCINOUS ADENOCARCINOMA               7                55
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    52   2   4   6
  2Q GAIN WILD-TYPE 271   2  21  19
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              52               271
  R1               2                 2
  R2               4                21
  RX               6                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     2
  2Q GAIN WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                          16    40
  2Q GAIN WILD-TYPE                        43   172
D4V12, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     16                43
  WHITE                                         40               172
[1] 4 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     2  53
  2Q GAIN WILD-TYPE   2 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   53
  2Q GAIN WILD-TYPE    2  216
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              53               216
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    34  11
  3P GAIN WILD-TYPE 301  90
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               45               391 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11                90 
$`3P GAIN MUTATED`
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3867 TCGA-AA-3976 TCGA-AZ-6608 TCGA-G4-6314 
       19.99        19.99        24.03        26.01         1.94        35.93 
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6140 
       12.66        43.76        37.02        36.53        29.16        24.13 
TCGA-A6-6650 TCGA-A6-6782 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3685 TCGA-AA-3842 
       20.61        20.28         2.01        14.01        37.05        37.02 
TCGA-AA-3971 TCGA-AA-A00F TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6899 
       16.08        34.03         1.02        33.04        41.00         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-A69D TCGA-AZ-6603 TCGA-CA-5254 
       22.42        26.47         0.95        17.85        29.56        12.69 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-6535 
       17.03        15.02        29.03        13.05        10.06        15.12 
TCGA-D5-6539 TCGA-D5-6924 TCGA-DM-A288 TCGA-F4-6704 TCGA-G4-6303 TCGA-G4-6323 
       12.49        14.30        14.04         1.55        65.85        13.78 
TCGA-G4-6626 TCGA-NH-A6GC TCGA-QL-A97D 
       46.75        12.79        21.90 

$`3P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        31.07        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       17.85        15.62         4.80         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 
       35.11        16.57        37.05        37.25        34.65        32.75 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 
       26.01        20.98        34.03         2.01        21.99        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07        35.01         1.02         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       83.24        24.53        27.42        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
        5.03        15.02        15.02        12.00        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       11.01        12.95        11.08        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       20.42        17.75        18.25        25.48        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
      133.18         8.35        82.39        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.43        26.04        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        38.70        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.95              0.00 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            65.85            148.01 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            19.99             22.36 
[1] "0.9 - 65.8 (20.0)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.4"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3P GAIN MUTATED         6        1        2        11         1         0
  3P GAIN WILD-TYPE      68        0       27       121         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           3          3          2          7        5
  3P GAIN WILD-TYPE        17          5         57         34       40
                   vv
clus                STAGE IVA STAGE IVB
  3P GAIN MUTATED           1         2
  3P GAIN WILD-TYPE        16         0
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  6                68
  STAGE IA                 1                 0
  STAGE II                 2                27
  STAGE IIA               11               121
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                3                17
  STAGE IIIA               3                 5
  STAGE IIIB               2                57
  STAGE IIIC               7                34
  STAGE IV                 5                40
  STAGE IVA                1                16
  STAGE IVB                2                 0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED     1   9  30   6
  3P GAIN WILD-TYPE  10  68 275  49
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               1                10
  T2               9                68
  T3              30               275
  T4               6                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  3P GAIN MUTATED    23  13  11
  3P GAIN WILD-TYPE 239  92  71
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              23               239
  N1              13                92
  N2              11                71
[1] 3 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    27   8
  3P GAIN WILD-TYPE 301  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     27    8
  3P GAIN WILD-TYPE  301   56
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              27               301
  1               8                56
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    24  23
  3P GAIN WILD-TYPE 189 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     24   23
  3P GAIN WILD-TYPE  189  213
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              24               189
  MALE                23               213
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    41   0
  3P GAIN WILD-TYPE 329   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     41    0
  3P GAIN WILD-TYPE  329    9
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               41               329
  YES               0                 9
[1] 2 2
[1] FALSE
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    41   5
  3P GAIN WILD-TYPE 341  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     41    5
  3P GAIN WILD-TYPE  341   57
                               clus
vv                              3P GAIN MUTATED 3P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       41               341
  COLON MUCINOUS ADENOCARCINOMA               5                57
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    32   1   2   3
  3P GAIN WILD-TYPE 291   3  23  22
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              32               291
  R1               1                 3
  R2               2                23
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  1     1
  3P GAIN WILD-TYPE                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           7    24
  3P GAIN WILD-TYPE                        52   188
D5V12, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      7                52
  WHITE                                         24               188
[1] 4 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     0  30
  3P GAIN WILD-TYPE   4 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   30
  3P GAIN WILD-TYPE    4  239
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              30               239
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    44  17
  3Q GAIN WILD-TYPE 291  84
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               61               375 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17                84 
$`3Q GAIN MUTATED`
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3867 TCGA-AA-3976 TCGA-AA-3979 
       13.02        19.99        19.99        24.03        26.01        24.00 
TCGA-AD-6888 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6314 TCGA-4T-AA8H 
       15.52         1.94         5.88        28.21        35.93        12.66 
TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6137 
        1.61        43.76        37.02        36.53        29.16        27.09 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 TCGA-AA-3532 TCGA-AA-3660 
       25.08        20.61        21.76        20.28        29.00        78.08 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3866 TCGA-AA-3971 
        2.01        14.01        37.05        37.02        17.03        16.08 
TCGA-AA-A00F TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 
       34.03         1.02        33.04        41.00         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6603 
       26.47        14.50         0.95        17.85         5.65        29.56 
TCGA-CA-5254 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       12.69         8.02        17.03        15.02        14.04        29.03 
TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6924 TCGA-DM-A288 
       13.05        10.06        15.12        12.49        14.30        14.04 
TCGA-F4-6704 TCGA-G4-6303 TCGA-G4-6311 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC 
        1.55        65.85        39.42        13.78        46.75        12.79 
TCGA-QL-A97D 
       21.90 

$`3Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3662 
       19.07        34.03         0.99        17.95        23.01         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       50.99        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 
       25.08        10.88        75.95       106.75       100.01        49.08 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       23.51        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT6 TCGA-5M-AATE 
       79.69        17.85        15.62         4.80         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 
       35.11        16.57        37.05        37.25        34.65        32.75 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6140 
       23.61        22.09        22.06        32.71        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
        8.38        25.18        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07         0.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       61.02         6.97        54.02        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01         5.98         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        36.95         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        31.00        38.07        35.01         1.02         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       12.16        83.24        24.53        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.92        27.09        16.31        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       25.48        43.27        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      131.51       135.65         7.76       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        67.30        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T 
       61.91        36.00        26.43        26.04        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        15.65        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        31.30        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       60.13        11.90        70.03 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.95              0.00 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            78.08            148.01 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            19.99             22.98 
[1] "0.9 - 78.1 (20.0)"  "0.0 - 148.0 (23.0)"
[1] "hr=" "1.7"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3Q GAIN MUTATED         8        1        4        13         1         0
  3Q GAIN WILD-TYPE      66        0       25       119         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           4          4          5          8        8
  3Q GAIN WILD-TYPE        16          4         54         33       37
                   vv
clus                STAGE IVA STAGE IVB
  3Q GAIN MUTATED           3         2
  3Q GAIN WILD-TYPE        14         0
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  8                66
  STAGE IA                 1                 0
  STAGE II                 4                25
  STAGE IIA               13               119
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                4                16
  STAGE IIIA               4                 4
  STAGE IIIB               5                54
  STAGE IIIC               8                33
  STAGE IV                 8                37
  STAGE IVA                3                14
  STAGE IVB                2                 0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q GAIN MUTATED     3  10  43   7
  3Q GAIN WILD-TYPE   8  67 262  48
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               3                 8
  T2              10                67
  T3              43               262
  T4               7                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  3Q GAIN MUTATED    30  21  13
  3Q GAIN WILD-TYPE 232  84  69
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              30               232
  N1              21                84
  N2              13                69
[1] 3 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    37  13
  3Q GAIN WILD-TYPE 291  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     37   13
  3Q GAIN WILD-TYPE  291   51
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              37               291
  1              13                51
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    32  32
  3Q GAIN WILD-TYPE 181 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     32   32
  3Q GAIN WILD-TYPE  181  204
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              32               181
  MALE                32               204
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    56   0
  3Q GAIN WILD-TYPE 314   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     56    0
  3Q GAIN WILD-TYPE  314    9
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               56               314
  YES               0                 9
[1] 2 2
[1] FALSE
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    57   6
  3Q GAIN WILD-TYPE 325  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     57    6
  3Q GAIN WILD-TYPE  325   56
                               clus
vv                              3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       57               325
  COLON MUCINOUS ADENOCARCINOMA               6                56
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    46   1   2   3
  3Q GAIN WILD-TYPE 277   3  23  22
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              46               277
  R1               1                 3
  R2               2                23
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  1     1
  3Q GAIN WILD-TYPE                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           8    34
  3Q GAIN WILD-TYPE                        51   178
D6V12, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      8                51
  WHITE                                         34               178
[1] 4 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     1  40
  3Q GAIN WILD-TYPE   3 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   40
  3Q GAIN WILD-TYPE    3  229
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              40               229
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     9   3
  4P GAIN WILD-TYPE 326  98
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               424 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                98 
$`4P GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3560 TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-A56B TCGA-AA-3982 
       45.60        19.99        15.62        43.76        56.25        27.02 
TCGA-AD-A5EK TCGA-AY-A8YK TCGA-CM-5862 TCGA-F4-6704 TCGA-G4-6307 TCGA-RU-A8FL 
       16.44        18.84         5.03         1.55        55.04        38.70 

$`4P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-4N-A93T 
       35.80        26.17        91.79        79.69        17.85         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 
       12.66         1.61         9.53        39.45        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        61.84         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       16.08        13.05        34.06        25.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 
       24.53         5.79        22.42        27.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.36        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       21.90        60.13        11.90        70.03 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             1.55              0.00 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            56.25            148.01 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           23.505            22.045 
[1] "1.6 - 56.2 (23.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4P GAIN MUTATED         2        0        0         1         0         0
  4P GAIN WILD-TYPE      72        1       29       131        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           0          0          4          2        1
  4P GAIN WILD-TYPE        20          8         55         39       44
                   vv
clus                STAGE IVA STAGE IVB
  4P GAIN MUTATED           2         0
  4P GAIN WILD-TYPE        15         2
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  2                72
  STAGE IA                 0                 1
  STAGE II                 0                29
  STAGE IIA                1               131
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                20
  STAGE IIIA               0                 8
  STAGE IIIB               4                55
  STAGE IIIC               2                39
  STAGE IV                 1                44
  STAGE IVA                2                15
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     0   2  10   0
  4P GAIN WILD-TYPE  11  75 295  55
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                11
  T2               2                75
  T3              10               295
  T4               0                55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4P GAIN MUTATED     3   4   5
  4P GAIN WILD-TYPE 259 101  77
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               3               259
  N1               4               101
  N2               5                77
[1] 3 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     6   3
  4P GAIN WILD-TYPE 322  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    3
  4P GAIN WILD-TYPE  322   61
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               6               322
  1               3                61
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   8
  4P GAIN WILD-TYPE 209 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    8
  4P GAIN WILD-TYPE  209  228
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               4               209
  MALE                 8               228
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    11   0
  4P GAIN WILD-TYPE 359   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    0
  4P GAIN WILD-TYPE  359    9
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               11               359
  YES               0                 9
[1] 2 2
[1] FALSE
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    11   1
  4P GAIN WILD-TYPE 371  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    1
  4P GAIN WILD-TYPE  371   61
                               clus
vv                              4P GAIN MUTATED 4P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       11               371
  COLON MUCINOUS ADENOCARCINOMA               1                61
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    11   0   0   0
  4P GAIN WILD-TYPE 312   4  25  25
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              11               312
  R1               0                 4
  R2               0                25
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  1     0
  4P GAIN WILD-TYPE                                0    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           5     4
  4P GAIN WILD-TYPE                        54   208
D7V12, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      5                54
  WHITE                                          4               208
[1] 4 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     0  10
  4P GAIN WILD-TYPE   4 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   10
  4P GAIN WILD-TYPE    4  259
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               259
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    10   6
  4Q GAIN WILD-TYPE 325  95
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               420 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6                95 
$`4Q GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3560 TCGA-AA-3867 TCGA-AA-3939 TCGA-A6-2671 
       24.33        45.60        19.99        24.03        12.99        43.76 
TCGA-A6-2686 TCGA-A6-A56B TCGA-AA-3982 TCGA-AD-A5EK TCGA-AY-A8YK TCGA-AZ-4614 
       37.02        56.25        27.02        16.44        18.84         5.65 
TCGA-AZ-6607 TCGA-F4-6704 TCGA-G4-6307 TCGA-RU-A8FL 
        3.19         1.55        55.04        38.70 

$`4Q GAIN WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
        0.99        13.02        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       14.93        31.07        29.98        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       79.69        17.85        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        9.53        39.45        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       61.84         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        17.85        19.33       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       47.41        35.31       133.18         8.35        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 
       67.30        65.85        53.62        44.68        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        21.90        60.13        11.90        70.03 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1.55              0.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            56.25            148.01 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            24.18             22.03 
[1] "1.6 - 56.2 (24.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.8"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4Q GAIN MUTATED         1        0        0         3         0         0
  4Q GAIN WILD-TYPE      73        1       29       129        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           0          0          4          3        4
  4Q GAIN WILD-TYPE        20          8         55         38       41
                   vv
clus                STAGE IVA STAGE IVB
  4Q GAIN MUTATED           2         0
  4Q GAIN WILD-TYPE        15         2
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                73
  STAGE IA                 0                 1
  STAGE II                 0                29
  STAGE IIA                3               129
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                20
  STAGE IIIA               0                 8
  STAGE IIIB               4                55
  STAGE IIIC               3                38
  STAGE IV                 4                41
  STAGE IVA                2                15
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     0   1  13   3
  4Q GAIN WILD-TYPE  11  76 292  52
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                11
  T2               1                76
  T3              13               292
  T4               3                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4Q GAIN MUTATED     4   5   8
  4Q GAIN WILD-TYPE 258 100  74
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               4               258
  N1               5               100
  N2               8                74
[1] 3 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     8   6
  4Q GAIN WILD-TYPE 320  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      8    6
  4Q GAIN WILD-TYPE  320   58
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               8               320
  1               6                58
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7  10
  4Q GAIN WILD-TYPE 206 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7   10
  4Q GAIN WILD-TYPE  206  226
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               7               206
  MALE                10               226
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    15   0
  4Q GAIN WILD-TYPE 355   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     15    0
  4Q GAIN WILD-TYPE  355    9
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               15               355
  YES               0                 9
[1] 2 2
[1] FALSE
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    16   1
  4Q GAIN WILD-TYPE 366  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     16    1
  4Q GAIN WILD-TYPE  366   61
                               clus
vv                              4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       16               366
  COLON MUCINOUS ADENOCARCINOMA               1                61
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    13   0   2   0
  4Q GAIN WILD-TYPE 310   4  23  25
D8V10, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              13               310
  R1               0                 4
  R2               2                23
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  1     0
  4Q GAIN WILD-TYPE                                0    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           4     7
  4Q GAIN WILD-TYPE                        55   205
D8V12, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      4                55
  WHITE                                          7               205
[1] 4 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     0  12
  4Q GAIN WILD-TYPE   4 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   12
  4Q GAIN WILD-TYPE    4  257
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              12               257
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    51  15
  5P GAIN WILD-TYPE 284  86
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               66               370 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               15                86 
$`5P GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3844 
       45.60        13.02        19.99        19.00        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3976 TCGA-AZ-6608 TCGA-DM-A285 TCGA-3L-AA1B 
       24.03        12.99        26.01         1.94         5.88        15.62 
TCGA-A6-2679 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-6650 
       44.91        37.25        37.02        34.65        32.45        20.61 
TCGA-A6-6651 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3678 TCGA-AA-3681 
       21.76        12.99        24.00         2.01        47.01         5.98 
TCGA-AA-3842 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3968 TCGA-AA-A029 TCGA-AA-A02E 
       37.02         0.99        17.03        21.99        51.98         2.96 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-5543 TCGA-AY-6196 
       40.96         5.79        16.44         0.92        33.01         0.20 
TCGA-AY-A8YK TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CM-4747 TCGA-CM-5860 
       18.84        49.41        29.56        12.69        25.02        32.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6678 TCGA-D5-5539 
       15.02        14.04        14.99        13.02        11.01        19.59 
TCGA-D5-6531 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6931 TCGA-DM-A1D8 TCGA-DM-A1DA 
       17.75        14.30        13.41        12.00        12.59         7.50 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6297 
       98.24        95.18        31.96         1.55        47.41        82.39 
TCGA-G4-6307 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-RU-A8FL 
       55.04        46.75        74.79        12.79         8.42        38.70 

$`5P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       34.03         0.99        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3870 
        0.92        36.00        85.05        19.04        31.07        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       24.00         2.01        50.99        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 
       75.95       106.75       100.01        49.08        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       79.69        17.85         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-3810 
       42.28        35.11        16.57        37.05        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.08        25.18        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 
       29.00        26.01        14.01        33.99        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 
       14.01        50.04        47.05        15.02        11.01        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        36.95         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       32.05        31.07        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
        2.01        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       37.02        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       41.00        39.98        18.05        12.16        83.24        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        26.47         0.46        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       16.31         0.95        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13        22.36        65.00        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 
       12.10         5.23        11.74         3.19        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       23.05        20.02        37.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 
        5.03        15.02        15.02        17.03        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       45.40        54.61        56.09        55.92        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43         9.04         9.44        11.64        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6461 
      119.93        35.97        60.79       117.07         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       43.04        33.67        13.25         0.53        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        8.35        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       13.78        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       15.65        16.80        42.77        29.46        32.98        31.30 
TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       21.90        60.13        11.90        70.03 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              0.2               0.0 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            98.24            148.01 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            19.02             22.75 
[1] "0.2 - 98.2 (19.0)"  "0.0 - 148.0 (22.8)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5P GAIN MUTATED         8        0        3        17         1         0
  5P GAIN WILD-TYPE      66        1       26       115         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           3          4          6         11        8
  5P GAIN WILD-TYPE        17          4         53         30       37
                   vv
clus                STAGE IVA STAGE IVB
  5P GAIN MUTATED           4         1
  5P GAIN WILD-TYPE        13         1
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  8                66
  STAGE IA                 0                 1
  STAGE II                 3                26
  STAGE IIA               17               115
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                3                17
  STAGE IIIA               4                 4
  STAGE IIIB               6                53
  STAGE IIIC              11                30
  STAGE IV                 8                37
  STAGE IVA                4                13
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P GAIN MUTATED     1  12  48   7
  5P GAIN WILD-TYPE  10  65 257  48
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                10
  T2              12                65
  T3              48               257
  T4               7                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5P GAIN MUTATED    29  21  18
  5P GAIN WILD-TYPE 233  84  64
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              29               233
  N1              21                84
  N2              18                64
[1] 3 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    44  13
  5P GAIN WILD-TYPE 284  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     44   13
  5P GAIN WILD-TYPE  284   51
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              44               284
  1              13                51
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    37  31
  5P GAIN WILD-TYPE 176 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     37   31
  5P GAIN WILD-TYPE  176  205
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              37               176
  MALE                31               205
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    54   1
  5P GAIN WILD-TYPE 316   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     54    1
  5P GAIN WILD-TYPE  316    8
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               54               316
  YES               1                 8
[1] 2 2
[1] FALSE
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    60   8
  5P GAIN WILD-TYPE 322  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     60    8
  5P GAIN WILD-TYPE  322   54
                               clus
vv                              5P GAIN MUTATED 5P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       60               322
  COLON MUCINOUS ADENOCARCINOMA               8                54
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    51   0   5   1
  5P GAIN WILD-TYPE 272   4  20  24
D9V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              51               272
  R1               0                 4
  R2               5                20
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  1     1
  5P GAIN WILD-TYPE                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          11    33
  5P GAIN WILD-TYPE                        48   179
D9V12, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     11                48
  WHITE                                         33               179
[1] 4 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     0  45
  5P GAIN WILD-TYPE   4 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0   45
  5P GAIN WILD-TYPE    4  224
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              45               224
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    29  10
  5Q GAIN WILD-TYPE 306  91
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               39               397 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               10                91 
$`5Q GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3976 
       45.60        19.00        19.04        14.93        12.99        26.01 
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-6650 
       15.62        44.91        37.25        34.65        32.45        20.61 
TCGA-AA-3666 TCGA-AA-3681 TCGA-AA-3842 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-A029 
        2.01         5.98        37.02         0.99        17.03        51.98 
TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-6598 
        2.96        40.96         5.79        16.44        33.01        49.41 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6167 
       29.56        11.74        32.02        15.02        14.04        14.99 
TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-DM-A1D8 TCGA-DM-A28M TCGA-G4-6626 
       11.01        19.59        17.75        12.59        95.18        46.75 
TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 
       74.79        12.79         8.42 

$`5Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
       19.99         6.05         0.92        36.00        85.05        19.04 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        24.00         2.01        50.99 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       17.85         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 
       35.11        16.57        37.05        37.02        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       78.08         6.97        54.02        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00        33.07         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 
       39.98        18.05        12.16        83.24        24.53        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       88.21         6.77        12.10         5.23         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.36        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       17.03        12.00        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       56.09        55.92        20.19        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.43        26.04        13.78        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98        31.30        21.90        38.70        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.99              0.00 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            95.18            148.01 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            19.00             22.36 
[1] "1.0 - 95.2 (19.0)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5Q GAIN MUTATED         6        0        3        10         1         0
  5Q GAIN WILD-TYPE      68        1       26       122         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           2          3          2          4        4
  5Q GAIN WILD-TYPE        18          5         57         37       41
                   vv
clus                STAGE IVA STAGE IVB
  5Q GAIN MUTATED           2         1
  5Q GAIN WILD-TYPE        15         1
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  6                68
  STAGE IA                 0                 1
  STAGE II                 3                26
  STAGE IIA               10               122
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                2                18
  STAGE IIIA               3                 5
  STAGE IIIB               2                57
  STAGE IIIC               4                37
  STAGE IV                 4                41
  STAGE IVA                2                15
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED     1   8  26   5
  5Q GAIN WILD-TYPE  10  69 279  50
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               1                10
  T2               8                69
  T3              26               279
  T4               5                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5Q GAIN MUTATED    20  14   6
  5Q GAIN WILD-TYPE 242  91  76
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              20               242
  N1              14                91
  N2               6                76
[1] 3 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    26   7
  5Q GAIN WILD-TYPE 302  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     26    7
  5Q GAIN WILD-TYPE  302   57
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              26               302
  1               7                57
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    21  19
  5Q GAIN WILD-TYPE 192 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     21   19
  5Q GAIN WILD-TYPE  192  217
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              21               192
  MALE                19               217
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    33   1
  5Q GAIN WILD-TYPE 337   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     33    1
  5Q GAIN WILD-TYPE  337    8
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               33               337
  YES               1                 8
[1] 2 2
[1] FALSE
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    36   4
  5Q GAIN WILD-TYPE 346  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     36    4
  5Q GAIN WILD-TYPE  346   58
                               clus
vv                              5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       36               346
  COLON MUCINOUS ADENOCARCINOMA               4                58
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    30   0   3   0
  5Q GAIN WILD-TYPE 293   4  22  25
D10V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              30               293
  R1               0                 4
  R2               3                22
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     0
  5Q GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           8    18
  5Q GAIN WILD-TYPE                        51   194
D10V12, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      8                51
  WHITE                                         18               194
[1] 4 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     0  25
  5Q GAIN WILD-TYPE   4 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   25
  5Q GAIN WILD-TYPE    4  244
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              25               244
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    62  18
  6P GAIN WILD-TYPE 273  83
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               80               356 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               18                83 
$`6P GAIN MUTATED`
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3697 TCGA-G4-6310 TCGA-G4-6625 TCGA-A6-2675 
       13.02        19.99        85.05        63.62        91.79        43.43 
TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       42.90        44.91        36.53        32.45        30.44        29.19 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-A56B TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
       25.08        20.61        56.25        29.00        29.00        12.99 
TCGA-AA-3553 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3842 
       24.00        15.02        37.05        10.06        35.05        37.02 
TCGA-AA-3846 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3982 
       17.03        27.02         2.01        20.98        21.99        27.02 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A01I TCGA-AA-A02E TCGA-AA-A03J 
        7.96        13.94        34.03        31.00         2.96        40.96 
TCGA-AD-6901 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4682 
       22.42        14.50         0.95         0.20        17.26        22.36 
TCGA-AZ-4684 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 
       65.00        14.30        15.62        21.99         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 
       29.06        30.08        32.02         5.03        15.02        13.02 
TCGA-CM-6170 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6539 
       15.02        19.59        55.92        25.48        17.13        12.49 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H 
        9.04        13.41        11.38         7.50        14.04       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 
       98.24        95.18         8.61        31.96        35.74         1.55 
TCGA-G4-6297 TCGA-G4-6311 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW 
       82.39        39.42        46.75        10.98        12.79        29.46 
TCGA-QL-A97D TCGA-RU-A8FL 
       21.90        38.70 

$`6P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        23.51        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       79.69        17.85        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 
        9.53        39.45        43.76        46.65        43.76        42.28 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.75        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        9.07        19.07         0.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3818 
       47.01        11.01         5.98         5.03        26.99         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 
       32.05         0.99        31.07        53.00        17.03        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 
       31.00        24.00        33.01        26.01        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
       16.08        13.05        34.06        25.02        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
       22.03        41.00        39.98        18.05        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
       24.53         5.79        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31        33.01        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.65        32.94         5.13        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       70.16        51.32        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       22.03        22.98        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       56.09        20.19        20.42        17.75        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12        17.85         4.80        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A 
       44.32       131.51       135.65         7.76       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6461 TCGA-F4-6463 
       81.37       119.93        35.97        60.79        11.11        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       85.48        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       74.79        18.18        19.33        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO 
       16.80        42.77        32.98         8.42        31.30        60.13 
TCGA-T9-A92H TCGA-WS-AB45 
       11.90        70.03 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              0.2               0.0 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           117.07            148.01 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            22.39             22.03 
[1] "0.2 - 117.1 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6P GAIN MUTATED        11        0        3        21         2         0
  6P GAIN WILD-TYPE      63        1       26       111         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           2          4         12         12        8
  6P GAIN WILD-TYPE        18          4         47         29       37
                   vv
clus                STAGE IVA STAGE IVB
  6P GAIN MUTATED           5         1
  6P GAIN WILD-TYPE        12         1
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 11                63
  STAGE IA                 0                 1
  STAGE II                 3                26
  STAGE IIA               21               111
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                2                18
  STAGE IIIA               4                 4
  STAGE IIIB              12                47
  STAGE IIIC              12                29
  STAGE IV                 8                37
  STAGE IVA                5                12
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED     2  13  60   9
  6P GAIN WILD-TYPE   9  64 245  46
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               2                 9
  T2              13                64
  T3              60               245
  T4               9                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  6P GAIN MUTATED    42  18  24
  6P GAIN WILD-TYPE 220  87  58
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              42               220
  N1              18                87
  N2              24                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"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    59  14
  6P GAIN WILD-TYPE 269  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     59   14
  6P GAIN WILD-TYPE  269   50
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              59               269
  1              14                50
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    36  48
  6P GAIN WILD-TYPE 177 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     36   48
  6P GAIN WILD-TYPE  177  188
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              36               177
  MALE                48               188
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    68   2
  6P GAIN WILD-TYPE 302   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     68    2
  6P GAIN WILD-TYPE  302    7
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               68               302
  YES               2                 7
[1] 2 2
[1] FALSE
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    74   9
  6P GAIN WILD-TYPE 308  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     74    9
  6P GAIN WILD-TYPE  308   53
                               clus
vv                              6P GAIN MUTATED 6P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       74               308
  COLON MUCINOUS ADENOCARCINOMA               9                53
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    63   0   6   3
  6P GAIN WILD-TYPE 260   4  19  22
D11V10, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              63               260
  R1               0                 4
  R2               6                19
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  1     1
  6P GAIN WILD-TYPE                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                          11    43
  6P GAIN WILD-TYPE                        48   169
D11V12, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     11                48
  WHITE                                         43               169
[1] 4 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     0  53
  6P GAIN WILD-TYPE   4 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   53
  6P GAIN WILD-TYPE    4  216
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              53               216
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    57  15
  6Q GAIN WILD-TYPE 278  86
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               72               364 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               15                86 
$`6Q GAIN MUTATED`
TCGA-AA-3562 TCGA-AA-3697 TCGA-G4-6310 TCGA-G4-6625 TCGA-A6-2675 TCGA-A6-2676 
       19.99        85.05        63.62        91.79        43.43        42.90 
TCGA-A6-2679 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6650 TCGA-AA-3532 
       44.91        30.44        29.19        25.08        20.61        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3679 TCGA-AA-3685 
       29.00        26.01        12.99        24.00        15.02        37.05 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3869 TCGA-AA-3930 
       10.06        35.05        37.02        17.03        27.02         2.01 
TCGA-AA-3955 TCGA-AA-A00F TCGA-AA-A01I TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 
       20.98        34.03        31.00         2.96        40.96        22.42 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4682 
       14.50         0.95         0.20        17.26         5.65        22.36 
TCGA-AZ-4684 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 
       65.00        14.30        15.62        21.99         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 TCGA-CM-6170 
       29.06        32.02         5.03        15.02        13.02        15.02 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6926 
       19.59        55.92        25.48        17.13        12.49         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28K 
       13.41        11.38         7.50        14.04       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-G4-6297 TCGA-G4-6299 
       95.18         8.61        31.96        35.74        82.39        74.56 
TCGA-G4-6311 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL 
       39.42        10.98        12.79        29.46        21.90        38.70 

$`6Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 
       19.99         6.05         0.92        19.00        36.00        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       26.17        79.69        17.85        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       42.28        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 
       27.09        22.52        24.13         8.38        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 
        0.00        14.01        33.99        21.01        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.05        47.01        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        5.03        26.99         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        36.95         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       53.00        17.03        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       83.24        24.53         5.79        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 
        0.46         0.92        27.09        16.31        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        32.94         5.13        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       70.16        51.32        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.03        22.98        30.08        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       54.61        56.09        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12        17.85         4.80        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        7.53        12.39        10.13        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.35        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6461 
       26.47        81.37       119.93        35.97        60.79        11.11 
TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
      133.18         8.35        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       55.04        85.48        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        46.75        74.79        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        15.65        16.80        42.77        32.98         8.42 
TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        60.13        11.90        70.03 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              0.2               0.0 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           117.07            148.01 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            22.39             22.03 
[1] "0.2 - 117.1 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6Q GAIN MUTATED        11        0        3        17         2         0
  6Q GAIN WILD-TYPE      63        1       26       115         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           2          4          9         11        7
  6Q GAIN WILD-TYPE        18          4         50         30       38
                   vv
clus                STAGE IVA STAGE IVB
  6Q GAIN MUTATED           6         1
  6Q GAIN WILD-TYPE        11         1
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 11                63
  STAGE IA                 0                 1
  STAGE II                 3                26
  STAGE IIA               17               115
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                2                18
  STAGE IIIA               4                 4
  STAGE IIIB               9                50
  STAGE IIIC              11                30
  STAGE IV                 7                38
  STAGE IVA                6                11
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED     2  13  51  10
  6Q GAIN WILD-TYPE   9  64 254  45
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               2                 9
  T2              13                64
  T3              51               254
  T4              10                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  6Q GAIN MUTATED    38  16  22
  6Q GAIN WILD-TYPE 224  89  60
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              38               224
  N1              16                89
  N2              22                60
[1] 3 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    52  14
  6Q GAIN WILD-TYPE 276  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     52   14
  6Q GAIN WILD-TYPE  276   50
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              52               276
  1              14                50
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    35  41
  6Q GAIN WILD-TYPE 178 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     35   41
  6Q GAIN WILD-TYPE  178  195
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              35               178
  MALE                41               195
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    61   2
  6Q GAIN WILD-TYPE 309   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     61    2
  6Q GAIN WILD-TYPE  309    7
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               61               309
  YES               2                 7
[1] 2 2
[1] FALSE
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    67   8
  6Q GAIN WILD-TYPE 315  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     67    8
  6Q GAIN WILD-TYPE  315   54
                               clus
vv                              6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       67               315
  COLON MUCINOUS ADENOCARCINOMA               8                54
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    57   0   5   3
  6Q GAIN WILD-TYPE 266   4  20  22
D12V10, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              57               266
  R1               0                 4
  R2               5                20
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     1
  6Q GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                          10    41
  6Q GAIN WILD-TYPE                        49   171
D12V12, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     10                49
  WHITE                                         41               171
[1] 4 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  49
  6Q GAIN WILD-TYPE   4 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   49
  6Q GAIN WILD-TYPE    4  220
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              49               220
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   182  55
  7P GAIN WILD-TYPE 153  46
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              237               199 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               55                46 
$`7P GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3524 
       45.60        13.94        24.16         1.02        58.03        36.03 
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       13.02        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3976 
       85.05        14.93        24.03        29.98        24.00        26.01 
TCGA-AA-A00L TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6608 
       38.04        21.37        15.52        75.95       106.75         1.94 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 
        5.88        28.21        23.51        63.62        35.93        91.79 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2671 
       17.85        15.62         4.80        12.66         1.61        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2685 TCGA-A6-2686 
       43.76        43.43        44.91        35.11        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       29.19        29.16        22.52        24.13        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       20.61        24.69        23.87        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       56.25         9.63         5.03         7.04         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3534 
       35.01         6.97        38.99         9.07         0.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3655 
       26.01        12.99        14.01        33.99        24.00        61.02 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3680 
       78.08        54.02         2.01        14.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        10.06        35.05         0.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       36.95        37.02         0.00        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3955 
       17.03        27.02        18.05        31.00        24.00        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       21.99        16.08        34.06        27.02        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       19.00        34.03        42.02        15.02        15.02        32.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       33.04        26.01        51.98         2.01         5.03         0.92 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       39.98        40.96        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        16.44        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4682 
        0.20        17.82        17.26        18.84       109.28        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        88.21        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        5.23         3.19        12.36        12.46        12.39        12.59 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 
       14.30        17.56       148.01        85.45        21.99        20.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        11.01        11.08        11.08        11.01        10.06 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        55.92        17.75        25.48        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
        4.80        17.13        12.49         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
       14.30         9.04        13.41        10.26        24.43        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        12.59         7.50        44.32       131.51 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
        7.76        14.04        35.97       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       31.96        35.74         1.55        33.67         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
      133.18        82.39        74.56        65.85        44.68        55.04 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 
       39.42        61.91        36.00        26.43        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5Z1 
       74.79        18.18         9.93        15.65        12.79         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       21.90        38.70        70.03 

$`7P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       24.33        14.53        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3672 
       19.07        34.03         0.99        17.95        23.01         0.92 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       19.04        19.04        31.07        12.99         2.01        50.99 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 
       24.00        19.07        21.99        39.06        25.08        10.88 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
      100.01        49.08        22.09        35.80        26.17        79.69 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
        9.53        39.45        46.65        42.90        42.28        16.57 
TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       37.05        32.75        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 
       32.71        27.09         8.38        21.76        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A567 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
       19.66        61.84         3.02        63.98         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       19.07        29.00        21.01        29.95        20.98        13.94 
TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3819 
        6.97        50.04        47.05        47.01        26.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        38.99         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3930 
       10.06         0.00        33.07        36.03        53.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 
       33.01        26.01        34.03         2.01        13.05        25.02 
TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
        7.96        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D 
       27.02         0.99        17.03        14.99        34.98        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02R 
        1.02         1.02        37.02         2.96        39.98        22.03 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5820 TCGA-AM-5821 
       41.00        18.05        12.16        83.24         0.46         0.92 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 
       27.09        21.44        17.85        19.33        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5254 
        5.65        32.94         5.13         6.77        11.74        12.69 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 
       12.59        12.20        12.76        10.06        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6166 
       37.02        26.04        30.08        15.02        12.00        21.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 
       13.02        14.04        12.95        13.05        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 
       54.61        56.09        20.19        20.42        18.25        17.85 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       16.14        15.58        12.39         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D9 
       12.00        11.38       119.70       130.65        13.32       140.38 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17        26.47        81.37       119.93        60.79 
TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       98.24        11.11        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6302 
       41.42        43.04        13.25        35.31         8.35        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       53.62        85.48        26.04        10.98        19.33        19.33 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO 
       16.80        42.77        29.46        32.98        31.30        60.13 
TCGA-T9-A92H 
       11.90 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 0 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           148.01            140.38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            22.52             21.99 
[1] "0.0 - 148.0 (22.5)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7P GAIN MUTATED        40        1       15        51         2         0
  7P GAIN WILD-TYPE      34        0       14        81         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED          12          8         39         26       30
  7P GAIN WILD-TYPE         8          0         20         15       15
                   vv
clus                STAGE IVA STAGE IVB
  7P GAIN MUTATED          12         1
  7P GAIN WILD-TYPE         5         1
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 40                34
  STAGE IA                 1                 0
  STAGE II                15                14
  STAGE IIA               51                81
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III               12                 8
  STAGE IIIA               8                 0
  STAGE IIIB              39                20
  STAGE IIIC              26                15
  STAGE IV                30                15
  STAGE IVA               12                 5
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P GAIN MUTATED     9  42 166  27
  7P GAIN WILD-TYPE   2  35 139  28
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               9                 2
  T2              42                35
  T3             166               139
  T4              27                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  7P GAIN MUTATED   121  72  52
  7P GAIN WILD-TYPE 141  33  30
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             121               141
  N1              72                33
  N2              52                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"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   167  43
  7P GAIN WILD-TYPE 161  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    167   43
  7P GAIN WILD-TYPE  161   21
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             167               161
  1              43                21
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   115 130
  7P GAIN WILD-TYPE  98 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    115  130
  7P GAIN WILD-TYPE   98  106
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             115                98
  MALE               130               106
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   202   6
  7P GAIN WILD-TYPE 168   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    202    6
  7P GAIN WILD-TYPE  168    3
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              202               168
  YES               6                 3
[1] 2 2
[1] FALSE
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   218  25
  7P GAIN WILD-TYPE 164  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    218   25
  7P GAIN WILD-TYPE  164   37
                               clus
vv                              7P GAIN MUTATED 7P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                      218               164
  COLON MUCINOUS ADENOCARCINOMA              25                37
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   175   3  16  10
  7P GAIN WILD-TYPE 148   1   9  15
D13V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             175               148
  R1               3                 1
  R2              16                 9
  RX              10                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     5
  7P GAIN WILD-TYPE                                0     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          36   120
  7P GAIN WILD-TYPE                        23    92
D13V12, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          5                 6
  BLACK OR AFRICAN AMERICAN                     36                23
  WHITE                                        120                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     2 152
  7P GAIN WILD-TYPE   2 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2  152
  7P GAIN WILD-TYPE    2  117
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO             152               117
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   166  48
  7Q GAIN WILD-TYPE 169  53
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              214               222 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48                53 
$`7Q GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3524 
       45.60        13.94        24.16         1.02        58.03        36.03 
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3697 
       13.02        19.99        19.99         6.05        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AD-6888 
       14.93        24.03        29.98        24.00         2.01        15.52 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       75.95       106.75         5.88        23.51        63.62        35.93 
TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2671 
       91.79        17.85        15.62        12.66         1.61        43.76 
TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 
       43.43        44.91        35.11        37.25        37.02        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 
       32.91        31.63        30.44        29.19        29.16        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        25.18        20.61        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        16.24        24.92         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        37.05        35.01         6.97        38.99         9.07 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 
       29.00        26.01        12.99        14.01        33.99        24.00 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3680 
       61.02        78.08         2.01        14.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 
        5.98        37.05         5.03        35.05         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3869 
       37.02         0.00        32.05         0.99        31.07        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       18.05        31.00        24.00        21.99        16.08        34.06 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       27.02        27.02        13.94        19.00        34.03        42.02 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 
       15.02        15.02        32.02        33.04        26.01        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6890 
        2.01         5.03         0.92        39.98        40.96        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 
       22.42        27.42        26.47        16.44         0.46        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
        0.95         0.20        17.82        17.26        18.84       109.28 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       22.36        65.00        62.79        88.21        49.41        12.10 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6719 
        5.23         3.19        12.36        12.46        12.39        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 
       17.56       148.01        85.45        21.99        20.02        25.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
        8.02        27.02        13.02        22.03        22.98        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5541 
       11.08        11.08        11.01        10.06        19.59        55.92 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       17.75        25.48        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 
       12.49         7.53        10.13        12.43        14.30        13.41 
TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       10.26        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28M 
        7.50        44.32       131.51         7.76        14.04        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6854 
        8.61        31.96        35.74         1.55        33.67         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41       133.18        82.39        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 
       55.04        39.42        61.91        36.00        26.43        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        74.79        18.18         9.93        15.65        12.79 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
        8.42        21.90        38.70        70.03 

$`7Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       24.33        14.53        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3672 
       19.07        34.03         0.99        17.95        23.01         0.92 
TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3972 
       19.00        19.04        19.04        31.07        12.99        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        25.08        10.88       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-4N-A93T 
       28.21        22.09        35.80        26.17        79.69         4.80 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        9.53        39.45        46.65        43.76        42.90        42.28 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5661 
       16.57        37.05        34.65        32.75        36.53        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 
       23.61        22.09        22.06        32.71        27.09         8.38 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.39        20.12        19.66        61.84        56.25 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
        3.02        63.98         1.02         1.02        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 
       29.00        21.01        29.95        20.98        13.94         6.97 
TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3811 
       54.02        50.04        47.05        47.01        26.99        10.06 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        38.99         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3864 
       17.03        10.06         0.00        33.07        36.03        53.00 
TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       17.03         2.01        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00E 
        2.01        13.05        25.02         7.96        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       14.99        34.98        10.98        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02         1.02        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 
        2.96        39.98        22.03        41.00        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 
       83.24         5.79         0.92        14.50        27.09        33.01 
TCGA-AY-6197 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       21.44        17.85        19.33        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5254 
       32.94         5.13         6.77        29.56        11.74        12.69 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 
       12.59        12.59        12.20        12.76        10.06        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 
       23.05        37.02        26.04        29.06        30.08        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.00        21.99        13.02        14.04        12.95        13.05 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       12.03        45.40        54.61        56.09        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 
       18.25        17.85        16.14        15.58        12.39         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        11.38       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A 
       24.43       130.65       140.38       135.65       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       11.11        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 
       43.04        13.25        35.31         8.35        67.30        53.62 
TCGA-G4-6309 TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A8F8 
       85.48        26.04        10.98        19.33        19.33        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H 
       42.77        29.46        32.98        31.30        60.13        11.90 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 0 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           148.01            140.38 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           22.195            22.045 
[1] "0.0 - 148.0 (22.2)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7Q GAIN MUTATED        38        1       14        47         2         0
  7Q GAIN WILD-TYPE      36        0       15        85         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED          11          5         34         23       27
  7Q GAIN WILD-TYPE         9          3         25         18       18
                   vv
clus                STAGE IVA STAGE IVB
  7Q GAIN MUTATED          12         1
  7Q GAIN WILD-TYPE         5         1
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 38                36
  STAGE IA                 1                 0
  STAGE II                14                15
  STAGE IIA               47                85
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III               11                 9
  STAGE IIIA               5                 3
  STAGE IIIB              34                25
  STAGE IIIC              23                18
  STAGE IV                27                18
  STAGE IVA               12                 5
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q GAIN MUTATED     9  35 152  25
  7Q GAIN WILD-TYPE   2  42 153  30
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               9                 2
  T2              35                42
  T3             152               153
  T4              25                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  7Q GAIN MUTATED   114  61  47
  7Q GAIN WILD-TYPE 148  44  35
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             114               148
  N1              61                44
  N2              47                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"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   149  40
  7Q GAIN WILD-TYPE 179  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    149   40
  7Q GAIN WILD-TYPE  179   24
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             149               179
  1              40                24
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   105 117
  7Q GAIN WILD-TYPE 108 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    105  117
  7Q GAIN WILD-TYPE  108  119
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             105               108
  MALE               117               119
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   181   5
  7Q GAIN WILD-TYPE 189   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    181    5
  7Q GAIN WILD-TYPE  189    4
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              181               189
  YES               5                 4
[1] 2 2
[1] FALSE
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   196  23
  7Q GAIN WILD-TYPE 186  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    196   23
  7Q GAIN WILD-TYPE  186   39
                               clus
vv                              7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                      196               186
  COLON MUCINOUS ADENOCARCINOMA              23                39
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   158   3  15  10
  7Q GAIN WILD-TYPE 165   1  10  15
D14V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             158               165
  R1               3                 1
  R2              15                10
  RX              10                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  1     4
  7Q GAIN WILD-TYPE                                0     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          33   108
  7Q GAIN WILD-TYPE                        26   104
D14V12, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 7
  BLACK OR AFRICAN AMERICAN                     33                26
  WHITE                                        108               104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 137
  7Q GAIN WILD-TYPE   2 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  137
  7Q GAIN WILD-TYPE    2  132
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO             137               132
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    99  28
  8P GAIN WILD-TYPE 236  73
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              127               309 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               28                73 
$`8P GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3524 TCGA-AA-3662 TCGA-AA-3692 
       24.33        13.94        24.16        36.03         6.05        36.00 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-A00Z TCGA-G4-6310 
       19.04        19.04        29.98        12.99        21.99        63.62 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5657 
       15.62        12.66        39.45        37.02        32.45        31.63 
TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3502 
       29.19        32.71        29.16         9.63         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        6.97         1.02        19.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3673 
       12.99        14.01        20.98         6.97        14.01        50.04 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 TCGA-AA-3875 
        5.03        10.06        17.03         0.00        31.07        18.05 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A01D 
       34.03         2.01        18.05         0.99        17.03        10.98 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O TCGA-AD-5900 
       37.02        51.98         2.96         5.03         0.92        12.16 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A54L 
        5.79        27.42        16.44        27.09        21.44        17.26 
TCGA-AY-A8YK TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
       18.84        32.94         5.13        22.36        65.00        88.21 
TCGA-AZ-6598 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       49.41         5.23         3.19        12.69        12.36        12.46 
TCGA-CA-6715 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
       12.59       148.01        51.32         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       25.02         8.02        27.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6677 
       17.03        15.02        29.03        14.99        12.99        11.08 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 
       55.92        20.19        17.75        25.48         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6924 TCGA-D5-7000 TCGA-DM-A0X9 
       16.14        15.58         7.53        14.30        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
       38.20         7.50        44.32        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 
        8.61        35.74         6.18        34.42        43.04         8.35 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6626 
       67.30        65.85        53.62        44.68        39.42        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       74.79        18.18        15.65        29.46        32.98         8.42 
TCGA-WS-AB45 
       70.03 

$`8P GAIN WILD-TYPE`
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       45.60        14.53         1.02        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3952 
       85.05        14.93        31.07        24.03        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
       50.99        26.01        24.00        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 
       17.85         4.80         1.61         9.53        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.05        37.25        34.65        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3510 TCGA-AA-3517 
        5.03         7.04         3.02        37.05        63.98        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
        1.02         9.07         0.00        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       29.95        13.94        61.02        78.08        54.02         2.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 
       15.95        38.99        36.95        37.02         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
        0.00        33.07        36.03        32.05         0.99        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        20.98        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       42.02        14.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02H 
        1.02        33.04         1.02        26.01        39.98         2.01 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 
       22.03        41.00        39.98        18.05        40.96        83.24 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       24.53        22.42        26.47         0.46         0.92        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D 
       16.31         0.95        33.01         0.20        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-5403 
       19.33       109.28        58.39         1.41         5.65        62.79 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 
        6.77        12.10        29.56        11.74        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        21.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       23.05        26.04        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       30.08        32.02         5.03        12.00        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 
       54.61        19.59        56.09        20.42        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       15.12        17.85        12.49        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.38        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59       140.38       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28M 
       14.04        26.47        81.37       119.93        60.79        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
       31.96        11.11        35.74        47.87         1.55        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       82.39        74.56        55.04        85.48        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       26.43        26.04        13.78        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D 
        9.93        12.79        16.80        42.77        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       38.70        60.13        11.90 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 0 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           148.01            140.38 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            19.04             23.05 
[1] "0.0 - 148.0 (19.0)" "0.0 - 140.4 (23.1)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8P GAIN MUTATED        25        0       11        37         2         1
  8P GAIN WILD-TYPE      49        1       18        95         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           4          1         18         12       15
  8P GAIN WILD-TYPE        16          7         41         29       30
                   vv
clus                STAGE IVA STAGE IVB
  8P GAIN MUTATED           5         0
  8P GAIN WILD-TYPE        12         2
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 25                49
  STAGE IA                 0                 1
  STAGE II                11                18
  STAGE IIA               37                95
  STAGE IIB                2                 8
  STAGE IIC                1                 0
  STAGE III                4                16
  STAGE IIIA               1                 7
  STAGE IIIB              18                41
  STAGE IIIC              12                29
  STAGE IV                15                30
  STAGE IVA                5                12
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED     3  24  94  13
  8P GAIN WILD-TYPE   8  53 211  42
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               3                 8
  T2              24                53
  T3              94               211
  T4              13                42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  8P GAIN MUTATED    83  26  25
  8P GAIN WILD-TYPE 179  79  57
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              83               179
  N1              26                79
  N2              25                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"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    95  20
  8P GAIN WILD-TYPE 233  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     95   20
  8P GAIN WILD-TYPE  233   44
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              95               233
  1              20                44
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    65  69
  8P GAIN WILD-TYPE 148 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     65   69
  8P GAIN WILD-TYPE  148  167
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              65               148
  MALE                69               167
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   106   4
  8P GAIN WILD-TYPE 264   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    106    4
  8P GAIN WILD-TYPE  264    5
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              106               264
  YES               4                 5
[1] 2 2
[1] FALSE
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   118  15
  8P GAIN WILD-TYPE 264  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    118   15
  8P GAIN WILD-TYPE  264   47
                               clus
vv                              8P GAIN MUTATED 8P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                      118               264
  COLON MUCINOUS ADENOCARCINOMA              15                47
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    94   0  10  10
  8P GAIN WILD-TYPE 229   4  15  15
D15V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              94               229
  R1               0                 4
  R2              10                15
  RX              10                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     4
  8P GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          18    68
  8P GAIN WILD-TYPE                        41   144
D15V12, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4                 7
  BLACK OR AFRICAN AMERICAN                     18                41
  WHITE                                         68               144
[1] 4 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     1  85
  8P GAIN WILD-TYPE   3 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   85
  8P GAIN WILD-TYPE    3  184
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              85               184
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   167  50
  8Q GAIN WILD-TYPE 168  51
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              217               219 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               50                51 
$`8Q GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3524 
       24.33        45.60        13.94        24.16         1.02        36.03 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3713 
       13.02        23.01        19.99         6.05        36.00        19.04 
TCGA-AA-3715 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3976 TCGA-AA-3979 
       19.04        24.03        29.98        12.99        26.01        24.00 
TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 
       21.99        15.52       106.75         5.88        23.51        63.62 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2675 
       15.62        12.66         1.61         9.53        39.45        43.43 
TCGA-A6-2680 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       35.11        37.25        37.02        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       31.63        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        25.18        20.61        24.69        23.87 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3511 
        9.63         5.03         1.02        37.05        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3660 
       12.99        14.01        33.99        24.00        20.98        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 
        5.98        37.05         5.03        10.06        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       17.03         0.00         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 
       18.05         2.01        34.03         2.01        16.08        34.06 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A01D 
       13.94        19.00        18.05         0.99        17.03        10.98 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       12.00        31.00         1.02        37.02        51.98         2.96 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 
        5.03         0.92        41.00        12.16         5.79        27.42 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L 
       16.44         0.92        27.09        16.31        21.44        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       18.84       109.28        32.94         5.13        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6718 
        3.19        12.69        12.36        12.46        12.59        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 
       14.30       148.01        15.62        51.32         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        25.02         8.02        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       17.03        15.02        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       13.02        11.08        54.61        56.09        55.92        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       17.75        25.48        43.27        15.12         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        9.04        13.41        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28F TCGA-DM-A28G 
      130.65       140.38         7.50        44.32        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24         8.61        31.96        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 
        6.18        34.42        43.04         8.35        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
       26.43        46.75        74.79        18.18        10.98         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       15.65        16.80        29.46        32.98         8.42        38.70 
TCGA-WS-AB45 
       70.03 

$`8Q GAIN WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       14.53        58.03        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 
       19.07        34.03         0.99        17.95        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 
       19.00        85.05        14.93        31.07        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       50.99        19.07        38.04        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 
       10.88        75.95       100.01         1.94        49.08        28.21 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       17.85         4.80        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3809 
       42.28        44.91        16.57        37.05        34.65        32.75 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 
       30.44        33.53        22.09        22.06        22.52         8.38 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       21.76        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 
       24.92        61.84        56.25         7.04         3.02        63.98 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3561 
       38.99         1.02         9.07        21.01        29.95        13.94 
TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3812 
       61.02         2.01        47.05        11.01        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
        0.00        10.06         0.00        33.07        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       53.00        31.00        24.00        33.01        26.01        20.98 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       21.99        13.05        25.02        27.02         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       42.02        14.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02        35.01        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       26.01        39.98         2.01        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 
       40.96        83.24        24.53        22.42        26.47         0.46 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D 
       14.50         0.95        33.01         0.20        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-5403 TCGA-AZ-6599 
       19.33        58.39         1.41         5.65        62.79         6.77 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4950 
       12.39        12.59        12.20        12.76        17.56        85.45 
TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       70.16        21.99        21.14        82.95       124.27        23.05 
TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       26.04        22.03        32.02        12.00        14.04        16.04 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6530 
       11.01        10.06        12.03        45.40        19.59        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       18.25        17.85        12.49        12.39         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       13.35        12.00        24.43        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       12.59       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 
       26.47        81.37       119.93        95.18        11.11        47.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        41.42        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 
       35.31       133.18        82.39        85.48        61.91        26.04 
TCGA-G4-6323 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z2 
       13.78        19.33        19.33        12.79        42.77        31.30 
TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       21.90        60.13        11.90 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                0                 0 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           148.01            139.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            21.44             22.09 
[1] "0.0 - 148.0 (21.4)" "0.0 - 139.2 (22.1)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8Q GAIN MUTATED        36        0       16        62         2         1
  8Q GAIN WILD-TYPE      38        1       13        70         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           9          5         30         22       28
  8Q GAIN WILD-TYPE        11          3         29         19       17
                   vv
clus                STAGE IVA STAGE IVB
  8Q GAIN MUTATED          11         0
  8Q GAIN WILD-TYPE         6         2
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 36                38
  STAGE IA                 0                 1
  STAGE II                16                13
  STAGE IIA               62                70
  STAGE IIB                2                 8
  STAGE IIC                1                 0
  STAGE III                9                11
  STAGE IIIA               5                 3
  STAGE IIIB              30                29
  STAGE IIIC              22                19
  STAGE IV                28                17
  STAGE IVA               11                 6
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q GAIN MUTATED     3  40 159  24
  8Q GAIN WILD-TYPE   8  37 146  31
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               3                 8
  T2              40                37
  T3             159               146
  T4              24                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  8Q GAIN MUTATED   128  51  47
  8Q GAIN WILD-TYPE 134  54  35
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             128               134
  N1              51                54
  N2              47                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"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   160  39
  8Q GAIN WILD-TYPE 168  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    160   39
  8Q GAIN WILD-TYPE  168   25
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             160               168
  1              39                25
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   104 122
  8Q GAIN WILD-TYPE 109 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    104  122
  8Q GAIN WILD-TYPE  109  114
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             104               109
  MALE               122               114
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   184   5
  8Q GAIN WILD-TYPE 186   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    184    5
  8Q GAIN WILD-TYPE  186    4
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              184               186
  YES               5                 4
[1] 2 2
[1] FALSE
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   202  22
  8Q GAIN WILD-TYPE 180  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    202   22
  8Q GAIN WILD-TYPE  180   40
                               clus
vv                              8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                      202               180
  COLON MUCINOUS ADENOCARCINOMA              22                40
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   158   1  17  14
  8Q GAIN WILD-TYPE 165   3   8  11
D16V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             158               165
  R1               1                 3
  R2              17                 8
  RX              14                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     6
  8Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          33   109
  8Q GAIN WILD-TYPE                        26   103
D16V12, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                 5
  BLACK OR AFRICAN AMERICAN                     33                26
  WHITE                                        109               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"
D16V13, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3 141
  8Q GAIN WILD-TYPE   1 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  141
  8Q GAIN WILD-TYPE    1  128
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO             141               128
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    52  27
  9P GAIN WILD-TYPE 283  74
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               79               357 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               27                74 
$`9P GAIN MUTATED`
TCGA-A6-2682 TCGA-AA-3520 TCGA-AA-3844 TCGA-AA-3976 TCGA-AA-A00Z TCGA-AZ-4313 
       13.94        24.03        14.93        26.01        21.99        75.95 
TCGA-DM-A285 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2679 
        5.88        91.79        17.85         1.61        43.76        44.91 
TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-6142 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A56B 
       37.02        31.63        25.08        20.28        16.24        56.25 
TCGA-AA-3488 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3558 
        5.03        29.00        29.00        14.01        33.99        20.98 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3848 TCGA-AA-3852 
       78.08         6.97         2.01        50.04        10.06         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3869 TCGA-AA-3994 TCGA-AA-A00Q TCGA-AA-A01C 
       36.03         0.99        27.02        27.02        42.02        15.02 
TCGA-AA-A01D TCGA-AA-A029 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AY-5543 
       10.98        51.98         5.79        22.42        16.44        33.01 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5796 TCGA-CK-5914 
        0.20        17.26        12.10        29.56        12.39        21.99 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       13.02        22.03         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6167 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6539 TCGA-D5-6928 
       29.03        14.99        19.59        17.75        12.49        11.64 
TCGA-D5-6929 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28K 
       13.41        12.59         7.50        14.04        26.47        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6704 TCGA-G4-6323 
       95.18         8.61        31.96         6.18         1.55        13.78 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QL-A97D TCGA-SS-A7HO 
       46.75        10.98        12.79        42.77        21.90        60.13 
TCGA-WS-AB45 
       70.03 

$`9P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
        2.01        50.99        24.00        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94        49.08        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-3L-AA1B TCGA-4N-A93T 
       22.09        35.80        26.17        79.69        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       12.66         9.53        39.45        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        35.11        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        32.75        36.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       29.16        27.09        22.52        24.13         8.38        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       19.66        24.92        61.84         9.63         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 
       38.99         1.02         9.07        19.07         0.00        26.01 
TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 
       12.99        21.01        24.00        29.95        13.94        61.02 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02        14.01        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       36.95        37.02         0.00        17.03         0.00        33.07 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 
       32.05        31.07        53.00        17.03        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       34.03        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        34.98        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F 
       33.04         1.02        26.01        37.02         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 
       18.05        40.96        12.16        83.24        24.53        27.42 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       26.47         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
        0.95        21.44        17.82        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 
       37.02        25.02        26.04         8.02        27.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       12.00        16.04        21.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       55.92        20.19        20.42        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6461 
       81.37       119.93        35.97        60.79       117.07        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        35.74        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       26.43        26.04        74.79        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        15.65        16.80        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H 
       31.30        38.70        11.90 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 0 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            98.24            148.01 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            17.85             23.05 
[1] "0.0 - 98.2 (17.9)"  "0.0 - 148.0 (23.1)"
[1] "hr=" "1.8"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9P GAIN MUTATED         9        1        6        18         3         0
  9P GAIN WILD-TYPE      65        0       23       114         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           1          3          8         13        9
  9P GAIN WILD-TYPE        19          5         51         28       36
                   vv
clus                STAGE IVA STAGE IVB
  9P GAIN MUTATED           5         1
  9P GAIN WILD-TYPE        12         1
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  9                65
  STAGE IA                 1                 0
  STAGE II                 6                23
  STAGE IIA               18               114
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                1                19
  STAGE IIIA               3                 5
  STAGE IIIB               8                51
  STAGE IIIC              13                28
  STAGE IV                 9                36
  STAGE IVA                5                12
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED     2  10  55  13
  9P GAIN WILD-TYPE   9  67 250  42
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               2                 9
  T2              10                67
  T3              55               250
  T4              13                42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  9P GAIN MUTATED    41  22  18
  9P GAIN WILD-TYPE 221  83  64
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              41               221
  N1              22                83
  N2              18                64
[1] 3 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    50  15
  9P GAIN WILD-TYPE 278  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     50   15
  9P GAIN WILD-TYPE  278   49
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              50               278
  1              15                49
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    40  41
  9P GAIN WILD-TYPE 173 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     40   41
  9P GAIN WILD-TYPE  173  195
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              40               173
  MALE                41               195
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    63   2
  9P GAIN WILD-TYPE 307   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     63    2
  9P GAIN WILD-TYPE  307    7
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               63               307
  YES               2                 7
[1] 2 2
[1] FALSE
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    63  18
  9P GAIN WILD-TYPE 319  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     63   18
  9P GAIN WILD-TYPE  319   44
                               clus
vv                              9P GAIN MUTATED 9P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       63               319
  COLON MUCINOUS ADENOCARCINOMA              18                44
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    59   0   4   3
  9P GAIN WILD-TYPE 264   4  21  22
D17V10, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              59               264
  R1               0                 4
  R2               4                21
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  1     1
  9P GAIN WILD-TYPE                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                          18    35
  9P GAIN WILD-TYPE                        41   177
D17V12, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     18                41
  WHITE                                         35               177
[1] 4 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  48
  9P GAIN WILD-TYPE   2 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   48
  9P GAIN WILD-TYPE    2  221
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              48               221
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    45  24
  9Q GAIN WILD-TYPE 290  77
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               69               367 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24                77 
$`9Q GAIN MUTATED`
TCGA-A6-2682 TCGA-AA-3844 TCGA-AA-A00Z TCGA-AZ-4313 TCGA-DM-A285 TCGA-G4-6625 
       13.94        14.93        21.99        75.95         5.88        91.79 
TCGA-NH-A8F7 TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-A565 
       17.85        43.76        44.91        37.02        31.63        16.24 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 
       56.25         5.03        29.00        29.00        14.01        33.99 
TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3848 
       20.98        78.08         6.97         2.01        50.04        10.06 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3869 TCGA-AA-3994 TCGA-AA-A004 
        0.00        36.03         0.99        27.02        27.02        13.94 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A029 TCGA-AD-6899 TCGA-AD-6901 
       42.02        15.02        10.98        51.98         5.79        22.42 
TCGA-AD-A5EK TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-6600 TCGA-CA-5796 
       16.44        33.01         0.20        17.26        12.10        12.39 
TCGA-CK-5914 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       21.99        13.02        22.03         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-D5-6531 TCGA-D5-6539 TCGA-D5-6928 
       14.04        29.03        14.99        17.75        12.49        11.64 
TCGA-D5-6929 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28K 
       13.41        12.59         7.50        14.04        26.47        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50U 
       95.18        31.96         6.18        13.78        46.75        10.98 
TCGA-NH-A6GC TCGA-QL-A97D TCGA-WS-AB45 
       12.79        21.90        70.03 

$`9Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       38.04        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01         1.94        49.08        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       63.62        35.93        22.09        35.80        26.17        79.69 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
       46.65        43.76        43.43        42.90        42.28        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.05        37.25        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        61.84         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 TCGA-AA-3542 
        1.02         9.07        19.07         0.00        26.01        12.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 
       21.01        24.00        29.95        13.94        61.02        54.02 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 
       37.02         0.00        17.03         0.00        33.07        32.05 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        17.03        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
        7.96        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 
       12.16        83.24        24.53        27.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.92        14.50        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.46        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 
       25.02        26.04         8.02        27.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       30.08        32.02        15.02        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       55.92        20.19        20.42        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        35.74        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T 
       61.91        36.00        26.43        26.04        74.79        18.18 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        38.70        60.13 
TCGA-T9-A92H 
       11.90 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                 0 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            98.24            148.01 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            17.03             23.51 
[1] "0.0 - 98.2 (17.0)"  "0.0 - 148.0 (23.5)"
[1] "hr=" "1.8"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9Q GAIN MUTATED         9        1        5        19         1         0
  9Q GAIN WILD-TYPE      65        0       24       113         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           1          1          7         11        8
  9Q GAIN WILD-TYPE        19          7         52         30       37
                   vv
clus                STAGE IVA STAGE IVB
  9Q GAIN MUTATED           4         1
  9Q GAIN WILD-TYPE        13         1
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  9                65
  STAGE IA                 1                 0
  STAGE II                 5                24
  STAGE IIA               19               113
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                19
  STAGE IIIA               1                 7
  STAGE IIIB               7                52
  STAGE IIIC              11                30
  STAGE IV                 8                37
  STAGE IVA                4                13
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED     2   8  50  10
  9Q GAIN WILD-TYPE   9  69 255  45
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               2                 9
  T2               8                69
  T3              50               255
  T4              10                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  9Q GAIN MUTATED    38  17  16
  9Q GAIN WILD-TYPE 224  88  66
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              38               224
  N1              17                88
  N2              16                66
[1] 3 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    46  13
  9Q GAIN WILD-TYPE 282  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     46   13
  9Q GAIN WILD-TYPE  282   51
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              46               282
  1              13                51
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    34  37
  9Q GAIN WILD-TYPE 179 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     34   37
  9Q GAIN WILD-TYPE  179  199
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              34               179
  MALE                37               199
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    54   2
  9Q GAIN WILD-TYPE 316   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     54    2
  9Q GAIN WILD-TYPE  316    7
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               54               316
  YES               2                 7
[1] 2 2
[1] FALSE
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    55  16
  9Q GAIN WILD-TYPE 327  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     55   16
  9Q GAIN WILD-TYPE  327   46
                               clus
vv                              9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       55               327
  COLON MUCINOUS ADENOCARCINOMA              16                46
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    52   0   4   3
  9Q GAIN WILD-TYPE 271   4  21  22
D18V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              52               271
  R1               0                 4
  R2               4                21
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     1
  9Q GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                          15    30
  9Q GAIN WILD-TYPE                        44   182
D18V12, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     15                44
  WHITE                                         30               182
[1] 4 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     1  40
  9Q GAIN WILD-TYPE   3 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   40
  9Q GAIN WILD-TYPE    3  229
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              40               229
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    23  12
  10P GAIN WILD-TYPE 312  89
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                35                401 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                 89 
$`10P GAIN MUTATED`
TCGA-A6-6649 TCGA-AA-3952 TCGA-G4-6625 TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE 
       24.16         2.01        91.79        12.66         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-6650 TCGA-A6-6782 TCGA-AA-3548 
       43.76        37.02        32.45        20.61        20.28        33.99 
TCGA-AA-3666 TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3869 TCGA-AY-4070 TCGA-AY-A54L 
        2.01         0.00        33.07        27.02        16.31        17.26 
TCGA-AY-A8YK TCGA-CA-5254 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6678 
       18.84        12.69        32.02         5.03        14.04        11.01 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6534 TCGA-D5-6924 TCGA-DM-A1D8 TCGA-DM-A1DA 
       19.59        56.09        43.27        14.30        12.59         7.50 
TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 TCGA-QL-A97D 
        8.61         1.55        74.56        36.00        21.90 

$`10P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       35.80        26.17        79.69        17.85        15.62         4.80 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
        9.53        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       44.91        35.11        16.57        37.05        37.25        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       78.08         6.97        54.02        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       17.98        15.95        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        17.03        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       26.47        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
        0.95        33.01         0.20        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.36        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       54.61        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 
       47.41        35.31       133.18         8.35        82.39        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       61.91        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        38.70        60.13        11.90        70.03 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  0 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             91.79             148.01 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             19.59              22.36 
[1] "0.0 - 91.8 (19.6)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.8"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10P GAIN MUTATED         4        0        0        12         1         0
  10P GAIN WILD-TYPE      70        1       29       120         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           2          1          3          7        4
  10P GAIN WILD-TYPE        18          7         56         34       41
                    vv
clus                 STAGE IVA STAGE IVB
  10P GAIN MUTATED           3         0
  10P GAIN WILD-TYPE        14         2
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   4                 70
  STAGE IA                  0                  1
  STAGE II                  0                 29
  STAGE IIA                12                120
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 2                 18
  STAGE IIIA                1                  7
  STAGE IIIB                3                 56
  STAGE IIIC                7                 34
  STAGE IV                  4                 41
  STAGE IVA                 3                 14
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED     1   3  30   4
  10P GAIN WILD-TYPE  10  74 275  51
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                1                 10
  T2                3                 74
  T3               30                275
  T4                4                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  10P GAIN MUTATED    18   7  13
  10P GAIN WILD-TYPE 244  98  69
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               18                244
  N1                7                 98
  N2               13                 69
[1] 3 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    24   7
  10P GAIN WILD-TYPE 304  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     24    7
  10P GAIN WILD-TYPE  304   57
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               24                304
  1                7                 57
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    17  21
  10P GAIN WILD-TYPE 196 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     17   21
  10P GAIN WILD-TYPE  196  215
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               17                196
  MALE                 21                215
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    29   0
  10P GAIN WILD-TYPE 341   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     29    0
  10P GAIN WILD-TYPE  341    9
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                29                341
  YES                0                  9
[1] 2 2
[1] FALSE
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    34   4
  10P GAIN WILD-TYPE 348  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     34    4
  10P GAIN WILD-TYPE  348   58
                               clus
vv                              10P GAIN MUTATED 10P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        34                348
  COLON MUCINOUS ADENOCARCINOMA                4                 58
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    27   1   2   2
  10P GAIN WILD-TYPE 296   3  23  23
D19V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               27                296
  R1                1                  3
  R2                2                 23
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  1     1
  10P GAIN WILD-TYPE                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           8    20
  10P GAIN WILD-TYPE                        51   192
D19V12, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       8                 51
  WHITE                                          20                192
[1] 4 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     2  26
  10P GAIN WILD-TYPE   2 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   26
  10P GAIN WILD-TYPE    2  243
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               26                243
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    17   5
  10Q GAIN WILD-TYPE 318  96
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                22                414 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 5                 96 
$`10Q GAIN MUTATED`
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-4107 TCGA-AA-3666 TCGA-AA-3851 
       12.66         1.61        39.45        32.45         2.01        33.07 
TCGA-AA-3869 TCGA-AA-3982 TCGA-AA-A01R TCGA-AY-A54L TCGA-AY-A8YK TCGA-CA-5254 
       27.02        27.02        35.01        17.26        18.84        12.69 
TCGA-CM-5860 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6924 TCGA-DM-A1D8 TCGA-DM-A1DA 
       32.02        11.01        19.59        14.30        12.59         7.50 
TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 TCGA-QL-A97D 
        1.55        74.56        36.00        21.90 

$`10Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 
       17.85        15.62         4.80         9.53        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       36.53        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       37.02         0.00        17.03        10.06         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        25.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       27.42        26.47        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82        17.85        19.33       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       39.42        61.91        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        38.70        60.13        11.90        70.03 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.55               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             74.56             148.01 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            19.215             22.090 
[1] "1.6 - 74.6 (19.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10Q GAIN MUTATED         3        0        0         6         0         0
  10Q GAIN WILD-TYPE      71        1       29       126        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           2          1          2          4        2
  10Q GAIN WILD-TYPE        18          7         57         37       43
                    vv
clus                 STAGE IVA STAGE IVB
  10Q GAIN MUTATED           2         0
  10Q GAIN WILD-TYPE        15         2
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   3                 71
  STAGE IA                  0                  1
  STAGE II                  0                 29
  STAGE IIA                 6                126
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 2                 18
  STAGE IIIA                1                  7
  STAGE IIIB                2                 57
  STAGE IIIC                4                 37
  STAGE IV                  2                 43
  STAGE IVA                 2                 15
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED     0   3  18   2
  10Q GAIN WILD-TYPE  11  74 287  53
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                 11
  T2                3                 74
  T3               18                287
  T4                2                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  10Q GAIN MUTATED    10   6   7
  10Q GAIN WILD-TYPE 252  99  75
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               10                252
  N1                6                 99
  N2                7                 75
[1] 3 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    13   4
  10Q GAIN WILD-TYPE 315  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     13    4
  10Q GAIN WILD-TYPE  315   60
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               13                315
  1                4                 60
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     9  14
  10Q GAIN WILD-TYPE 204 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      9   14
  10Q GAIN WILD-TYPE  204  222
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                9                204
  MALE                 14                222
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    17   1
  10Q GAIN WILD-TYPE 353   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     17    1
  10Q GAIN WILD-TYPE  353    8
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                17                353
  YES                1                  8
[1] 2 2
[1] FALSE
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    19   4
  10Q GAIN WILD-TYPE 363  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     19    4
  10Q GAIN WILD-TYPE  363   58
                               clus
vv                              10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        19                363
  COLON MUCINOUS ADENOCARCINOMA                4                 58
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    16   0   1   2
  10Q GAIN WILD-TYPE 307   4  24  23
D20V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               16                307
  R1                0                  4
  R2                1                 24
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  1     1
  10Q GAIN WILD-TYPE                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           6    10
  10Q GAIN WILD-TYPE                        53   202
D20V12, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       6                 53
  WHITE                                          10                202
[1] 4 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     2  14
  10Q GAIN WILD-TYPE   2 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   14
  10Q GAIN WILD-TYPE    2  255
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               14                255
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    38  15
  11P GAIN WILD-TYPE 297  86
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                53                383 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                 86 
$`11P GAIN MUTATED`
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3867 TCGA-AD-6888 TCGA-AZ-6608 TCGA-G4-6310 
       13.02        19.99        24.03        15.52         1.94        63.62 
TCGA-G4-6314 TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-5660 
       35.93         1.61        43.76        43.43        44.91        29.19 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3494 
       25.08        25.18        23.87        56.25         5.03         1.02 
TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 
       12.99        24.00        50.04        37.02        17.03        33.07 
TCGA-AA-3856 TCGA-AA-3875 TCGA-AA-3955 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A02F 
        0.99        18.05        20.98        27.02        34.03        39.98 
TCGA-AD-6901 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 
       22.42        16.31         0.95        18.84        65.00        62.79 
TCGA-AZ-6603 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 
       29.56       148.01         8.02        17.03        29.03        21.99 
TCGA-CM-6677 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6929 TCGA-DM-A1D6 
       11.08        25.48        17.85         7.53        13.41        49.91 
TCGA-DM-A28F TCGA-G4-6303 TCGA-G4-6307 TCGA-QG-A5YW TCGA-RU-A8FL 
       35.97        65.85        55.04        29.46        38.70 

$`11P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        31.07        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       21.99        39.06        21.37        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01        49.08         5.88        28.21        23.51 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
       15.62         4.80        12.66         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.76        42.90        42.28        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       37.25        37.02        34.65        32.75        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
        8.38        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU 
       19.66        20.28        16.24        24.92        61.84         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        26.01        14.01        33.99        21.01 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       38.99        36.95         0.00        10.06         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       36.03        32.05        31.07        53.00        17.03        27.02 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        26.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
       24.53         5.79        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.92        14.50        27.09        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        17.85        19.33       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
        1.41         5.65        32.94         5.13        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        14.04        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
      119.93        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 
       74.56        67.30        53.62        44.68        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        16.80        42.77        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        60.13        11.90        70.03 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.95               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            148.01             140.38 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             25.08              21.99 
[1] "0.9 - 148.0 (25.1)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11P GAIN MUTATED         6        0        2         8         1         0
  11P GAIN WILD-TYPE      68        1       27       124         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           1          3          9          7        9
  11P GAIN WILD-TYPE        19          5         50         34       36
                    vv
clus                 STAGE IVA STAGE IVB
  11P GAIN MUTATED           5         0
  11P GAIN WILD-TYPE        12         2
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   6                 68
  STAGE IA                  0                  1
  STAGE II                  2                 27
  STAGE IIA                 8                124
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 19
  STAGE IIIA                3                  5
  STAGE IIIB                9                 50
  STAGE IIIC                7                 34
  STAGE IV                  9                 36
  STAGE IVA                 5                 12
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED     3   8  41   2
  11P GAIN WILD-TYPE   8  69 264  53
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                3                  8
  T2                8                 69
  T3               41                264
  T4                2                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  11P GAIN MUTATED    22  17  15
  11P GAIN WILD-TYPE 240  88  67
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               22                240
  N1               17                 88
  N2               15                 67
[1] 3 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    31  14
  11P GAIN WILD-TYPE 297  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     31   14
  11P GAIN WILD-TYPE  297   50
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               31                297
  1               14                 50
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    25  29
  11P GAIN WILD-TYPE 188 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     25   29
  11P GAIN WILD-TYPE  188  207
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               25                188
  MALE                 29                207
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    47   1
  11P GAIN WILD-TYPE 323   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     47    1
  11P GAIN WILD-TYPE  323    8
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                47                323
  YES                1                  8
[1] 2 2
[1] FALSE
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    51   2
  11P GAIN WILD-TYPE 331  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     51    2
  11P GAIN WILD-TYPE  331   60
                               clus
vv                              11P GAIN MUTATED 11P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        51                331
  COLON MUCINOUS ADENOCARCINOMA                2                 60
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    36   1   4   1
  11P GAIN WILD-TYPE 287   3  21  24
D21V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               36                287
  R1                1                  3
  R2                4                 21
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           7    30
  11P GAIN WILD-TYPE                        52   182
D21V12, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       7                 52
  WHITE                                          30                182
[1] 4 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  35
  11P GAIN WILD-TYPE   3 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   35
  11P GAIN WILD-TYPE    3  234
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               35                234
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    39  11
  11Q GAIN WILD-TYPE 296  90
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                50                386 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                 90 
$`11Q GAIN MUTATED`
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3867 TCGA-AZ-6608 TCGA-G4-6310 TCGA-G4-6314 
       13.02        19.99        24.03         1.94        63.62        35.93 
TCGA-5M-AAT4 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6142 
        1.61        43.43        44.91        29.19        29.16        25.08 
TCGA-A6-6648 TCGA-A6-A56B TCGA-AA-3494 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3553 
       25.18        56.25         1.02        29.00        12.99        24.00 
TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       50.04        37.05        37.02        17.03        10.06        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3955 TCGA-AA-3982 TCGA-AA-A00F TCGA-AY-4070 
        0.99        31.07        20.98        27.02        34.03        16.31 
TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-CK-4948 TCGA-CM-4750 
       18.84        65.00        62.79        29.56       148.01         8.02 
TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-5541 TCGA-D5-6533 
       17.03        29.03        21.99        11.08        55.92        25.48 
TCGA-D5-6898 TCGA-D5-6929 TCGA-DM-A1D8 TCGA-DM-A28F TCGA-G4-6303 TCGA-G4-6307 
        7.53        13.41        12.59        35.97        65.85        55.04 
TCGA-QG-A5YW TCGA-RU-A8FL 
       29.46        38.70 

$`11Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        31.07        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       75.95       106.75       100.01        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       23.51        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE 
       17.85        15.62         4.80        12.66         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
       43.76        46.65        43.76        42.90        42.28        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       36.53        32.45        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       61.84         9.63         5.03         7.04         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 
        9.07        19.07         0.00        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       78.08         6.97        54.02         2.01        14.01        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
       15.95        38.99        36.95         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       36.03        32.05        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 
       31.00         2.01        24.00        33.01        26.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       16.44         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       33.01         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        88.21        49.41         6.77        12.10 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        54.61        19.59        56.09        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
      133.18         8.35        82.39        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO 
       42.77        32.98         8.42        31.30        21.90        60.13 
TCGA-T9-A92H TCGA-WS-AB45 
       11.90        70.03 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.99               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            148.01             140.38 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             28.01              21.83 
[1] "1.0 - 148.0 (28.0)" "0.0 - 140.4 (21.8)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11Q GAIN MUTATED         5        0        3         7         1         0
  11Q GAIN WILD-TYPE      69        1       26       125         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           1          3          9          8        6
  11Q GAIN WILD-TYPE        19          5         50         33       39
                    vv
clus                 STAGE IVA STAGE IVB
  11Q GAIN MUTATED           5         0
  11Q GAIN WILD-TYPE        12         2
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   5                 69
  STAGE IA                  0                  1
  STAGE II                  3                 26
  STAGE IIA                 7                125
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 19
  STAGE IIIA                3                  5
  STAGE IIIB                9                 50
  STAGE IIIC                8                 33
  STAGE IV                  6                 39
  STAGE IVA                 5                 12
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED     1   9  39   2
  11Q GAIN WILD-TYPE  10  68 266  53
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                1                 10
  T2                9                 68
  T3               39                266
  T4                2                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  11Q GAIN MUTATED    20  17  14
  11Q GAIN WILD-TYPE 242  88  68
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               20                242
  N1               17                 88
  N2               14                 68
[1] 3 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    31  11
  11Q GAIN WILD-TYPE 297  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     31   11
  11Q GAIN WILD-TYPE  297   53
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               31                297
  1               11                 53
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    24  27
  11Q GAIN WILD-TYPE 189 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     24   27
  11Q GAIN WILD-TYPE  189  209
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               24                189
  MALE                 27                209
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    45   1
  11Q GAIN WILD-TYPE 325   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     45    1
  11Q GAIN WILD-TYPE  325    8
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                45                325
  YES                1                  8
[1] 2 2
[1] FALSE
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    50   1
  11Q GAIN WILD-TYPE 332  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     50    1
  11Q GAIN WILD-TYPE  332   61
                               clus
vv                              11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        50                332
  COLON MUCINOUS ADENOCARCINOMA                1                 61
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    37   1   2   1
  11Q GAIN WILD-TYPE 286   3  23  24
D22V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               37                286
  R1                1                  3
  R2                2                 23
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           7    26
  11Q GAIN WILD-TYPE                        52   186
D22V12, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       7                 52
  WHITE                                          26                186
[1] 4 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  32
  11Q GAIN WILD-TYPE   3 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   32
  11Q GAIN WILD-TYPE    3  237
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               32                237
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    66  21
  12P GAIN WILD-TYPE 269  80
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                87                349 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                21                 80 
$`12P GAIN MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3715 
       13.94        14.53        58.03        19.99         0.92        19.04 
TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3950 TCGA-AZ-6608 TCGA-3L-AA1B TCGA-4T-AA8H 
       14.93        12.99        24.00         1.94        15.62        12.66 
TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 
       44.91        37.02        32.75        22.09        25.08        20.61 
TCGA-A6-6780 TCGA-A6-A566 TCGA-AA-3494 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       20.12        24.92         1.02         0.00        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3660 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       12.99        78.08        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3851 
       26.99        35.05         0.99        37.02         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I 
        0.00        24.00        26.01        18.05        12.00        31.00 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       51.98         0.92        22.03        39.98        40.96        12.16 
TCGA-AD-6963 TCGA-AM-5821 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-6598 TCGA-AZ-6599 
       27.42         0.92         0.20        18.84        49.41         6.77 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        3.19        12.69        12.36       148.01        85.45        15.62 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6166 TCGA-CM-6169 
       20.02        25.02        32.02        15.02        21.99        13.02 
TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6924 
       14.04        11.01        20.19        17.75         4.80        14.30 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.41        12.00        10.26       119.70        24.43 
TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6703 TCGA-G4-6306 TCGA-G4-6323 
       44.32        95.18         8.61        47.87        44.68        13.78 
TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A6GB 
       74.79        10.98        15.65 

$`12P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        17.95        23.01        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        85.05        19.04        31.07        24.03        29.98 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       75.95       106.75       100.01        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 
       91.79        79.69        17.85         4.80         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       42.28        35.11        16.57        37.05        37.25        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        23.61        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52        24.13         8.38        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 
       24.39        23.87        19.66        20.28        16.24        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       56.25         9.63         5.03         7.04         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
        9.07        19.07        26.01        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       15.02        10.06        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 
       38.99        36.95        17.03        10.06         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       18.05        31.00         2.01        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E 
        1.02        33.04         1.02        26.01        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6889 
       39.98         2.01         5.03        41.00        18.05        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
       24.53         5.79        22.42        26.47        16.44         0.46 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        17.85        19.33       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        12.10        29.56         5.23        11.74 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5914 
       10.06        14.30        17.56        70.16        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         2.01       124.27        23.05        37.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        12.00        14.04        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.42        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       13.35        11.38        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 
       35.97        60.79       117.07        98.24        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       26.43        26.04        46.75        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        31.30        21.90        38.70        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  0 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            148.01             140.38 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             18.84              23.51 
[1] "0.0 - 148.0 (18.8)" "0.0 - 140.4 (23.5)"
[1] "hr=" "1.2"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12P GAIN MUTATED        12        1        8        35         2         0
  12P GAIN WILD-TYPE      62        0       21        97         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           4          2          6          9        6
  12P GAIN WILD-TYPE        16          6         53         32       39
                    vv
clus                 STAGE IVA STAGE IVB
  12P GAIN MUTATED           6         0
  12P GAIN WILD-TYPE        11         2
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  12                 62
  STAGE IA                  1                  0
  STAGE II                  8                 21
  STAGE IIA                35                 97
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 4                 16
  STAGE IIIA                2                  6
  STAGE IIIB                6                 53
  STAGE IIIC                9                 32
  STAGE IV                  6                 39
  STAGE IVA                 6                 11
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED     0  15  64  13
  12P GAIN WILD-TYPE  11  62 241  42
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                0                 11
  T2               15                 62
  T3               64                241
  T4               13                 42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12P GAIN MUTATED    62  17  14
  12P GAIN WILD-TYPE 200  88  68
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               62                200
  N1               17                 88
  N2               14                 68
[1] 3 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    68  12
  12P GAIN WILD-TYPE 260  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     68   12
  12P GAIN WILD-TYPE  260   52
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               68                260
  1               12                 52
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    45  48
  12P GAIN WILD-TYPE 168 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     45   48
  12P GAIN WILD-TYPE  168  188
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               45                168
  MALE                 48                188
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    70   2
  12P GAIN WILD-TYPE 300   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     70    2
  12P GAIN WILD-TYPE  300    7
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                70                300
  YES                2                  7
[1] 2 2
[1] FALSE
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    77  16
  12P GAIN WILD-TYPE 305  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     77   16
  12P GAIN WILD-TYPE  305   46
                               clus
vv                              12P GAIN MUTATED 12P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        77                305
  COLON MUCINOUS ADENOCARCINOMA               16                 46
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    71   1   3   4
  12P GAIN WILD-TYPE 252   3  22  21
D23V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               71                252
  R1                1                  3
  R2                3                 22
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     2
  12P GAIN WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          11    41
  12P GAIN WILD-TYPE                        48   171
D23V12, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      11                 48
  WHITE                                          41                171
[1] 4 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     0  53
  12P GAIN WILD-TYPE   4 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   53
  12P GAIN WILD-TYPE    4  216
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               53                216
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    66  18
  12Q GAIN WILD-TYPE 269  83
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                84                352 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                 83 
$`12Q GAIN MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3715 
       13.94        14.53        58.03        19.99         0.92        19.04 
TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 TCGA-AZ-6608 TCGA-3L-AA1B 
       14.93        12.99        24.00        26.01         1.94        15.62 
TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5664 TCGA-A6-6142 
       12.66        44.91        37.02        32.75        22.09        25.08 
TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-A566 TCGA-AA-3494 TCGA-AA-3529 TCGA-AA-3532 
       20.61        20.12        24.92         1.02         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       29.00        12.99        78.08         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3851 
       26.99        35.05         0.99        37.02         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A01G 
        0.00        24.00        26.01        18.05        18.05        12.00 
TCGA-AA-A01I TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J 
       31.00        51.98         0.92        22.03        39.98        40.96 
TCGA-AD-5900 TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5254 
       12.16         0.92        18.84        49.41         6.77        12.69 
TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-4747 TCGA-CM-5860 
       12.36       148.01        85.45        15.62        25.02        32.02 
TCGA-CM-5863 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6529 
       15.02        21.99        13.02        14.04        11.01        20.19 
TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-7000 
       17.75         4.80        14.30        11.64        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6463 TCGA-F4-6703 
      119.70        24.43        44.32        95.18        35.74        47.87 
TCGA-G4-6306 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A6GB TCGA-QL-A97D 
       44.68        13.78        74.79        10.98        15.65        21.90 

$`12Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        17.95        23.01        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        85.05        19.04        31.07        24.03        29.98 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       79.69        17.85         4.80         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 
       35.11        16.57        37.05        37.25        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B 
       23.87        19.66        20.28        16.24        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
        9.63         5.03         7.04         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       19.07        26.01        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        61.02         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       11.01        10.06        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 
       38.99        36.95        17.03        10.06         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       18.05        31.00         2.01        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       30.02        34.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       32.02        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F 
       33.04         1.02        26.01        37.02         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6890 
        2.01         5.03        41.00        18.05        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       21.44        17.82        17.26        17.85        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        88.21        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4951 
       12.20        12.76        10.06        14.30        17.56        70.16 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       23.05        20.02        37.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       45.40        54.61        19.59        56.09        55.92        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25        25.48        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
       12.43         9.04         9.44        13.41        13.35        11.38 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
      117.07        98.24         8.61        31.96        11.11        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       82.39        74.56        67.30        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
       46.75        18.18        19.33        19.33         9.93        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       38.70        60.13        11.90        70.03 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  0 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            148.01             140.38 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            20.055             22.995 
[1] "0.0 - 148.0 (20.1)" "0.0 - 140.4 (23.0)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12Q GAIN MUTATED        12        1        7        36         2         0
  12Q GAIN WILD-TYPE      62        0       22        96         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           3          3          6          8        3
  12Q GAIN WILD-TYPE        17          5         53         33       42
                    vv
clus                 STAGE IVA STAGE IVB
  12Q GAIN MUTATED           6         0
  12Q GAIN WILD-TYPE        11         2
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  12                 62
  STAGE IA                  1                  0
  STAGE II                  7                 22
  STAGE IIA                36                 96
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 3                 17
  STAGE IIIA                3                  5
  STAGE IIIB                6                 53
  STAGE IIIC                8                 33
  STAGE IV                  3                 42
  STAGE IVA                 6                 11
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED     0  16  59  12
  12Q GAIN WILD-TYPE  11  61 246  43
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                0                 11
  T2               16                 61
  T3               59                246
  T4               12                 43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12Q GAIN MUTATED    61  18   9
  12Q GAIN WILD-TYPE 201  87  73
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               61                201
  N1               18                 87
  N2                9                 73
[1] 3 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    67   9
  12Q GAIN WILD-TYPE 261  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     67    9
  12Q GAIN WILD-TYPE  261   55
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               67                261
  1                9                 55
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    43  45
  12Q GAIN WILD-TYPE 170 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     43   45
  12Q GAIN WILD-TYPE  170  191
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               43                170
  MALE                 45                191
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    68   2
  12Q GAIN WILD-TYPE 302   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     68    2
  12Q GAIN WILD-TYPE  302    7
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                68                302
  YES                2                  7
[1] 2 2
[1] FALSE
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    71  17
  12Q GAIN WILD-TYPE 311  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     71   17
  12Q GAIN WILD-TYPE  311   45
                               clus
vv                              12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        71                311
  COLON MUCINOUS ADENOCARCINOMA               17                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    68   1   2   4
  12Q GAIN WILD-TYPE 255   3  23  21
D24V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               68                255
  R1                1                  3
  R2                2                 23
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     2
  12Q GAIN WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          12    36
  12Q GAIN WILD-TYPE                        47   176
D24V12, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      12                 47
  WHITE                                          36                176
[1] 4 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     0  49
  12Q GAIN WILD-TYPE   4 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   49
  12Q GAIN WILD-TYPE    4  220
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               49                220
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED   194  53
  13Q GAIN WILD-TYPE 141  48
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               247                189 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                53                 48 
$`13Q GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3560 
       24.03        36.03        34.03         0.99        13.02        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
       19.99         6.05        19.00        85.05        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 
       24.03        29.98        12.99        50.99        26.01        19.07 
TCGA-AA-A00L TCGA-AD-6548 TCGA-AZ-4313 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       38.04        21.37        75.95         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A8F7 
       28.21        23.51        63.62        35.80        91.79        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       46.65        43.76        42.28        44.91        35.11        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       34.65        36.53        32.45        32.91        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       23.87        20.28        61.84         9.63         5.03         7.04 
TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3534 
       37.05         6.97        38.99         9.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       20.98        13.94        78.08         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       15.02         5.98        37.05        10.06        35.05         0.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 
       36.95        37.02        17.03        10.06        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 
       31.07        17.03        27.02         2.01        24.00        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3982 TCGA-AA-3989 
       20.98        34.03        16.08        13.05        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00W 
       27.02        13.94        19.00        34.03        42.02        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
       15.02        15.02        32.02        12.00        31.00        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.96        39.98         2.01        41.00        39.98        40.96 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       16.31         0.95        33.01        21.44        17.26        18.84 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
      109.28         1.41         5.13        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
       49.41        12.10        29.56         5.23        11.74        12.69 
TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-6748 
       12.36        12.59        14.30        17.56       148.01         2.01 
TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02         8.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        32.02         5.03        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        11.01        11.08        11.08        11.01        10.06 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       12.49         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 
       13.41        12.00        11.38        10.26       119.70       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 
       92.75        49.91        13.32         7.50       131.51         7.76 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 
       14.04        26.47       119.93        35.97        31.96         6.18 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       41.42        43.04        33.67         0.53        47.41       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 
        8.35        82.39        74.56        65.85        44.68        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       36.00        26.43        46.75        74.79        18.18        19.33 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL 
       15.65        16.80        42.77        29.46        21.90        38.70 
TCGA-SS-A7HO 
       60.13 

$`13Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3554 
       24.33        13.02        37.05         8.05        19.07        17.95 
TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3950 
       23.01         0.92        36.00        19.04        31.07        24.00 
TCGA-AA-3952 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 
        2.01        24.00        21.99        39.06        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6588 
       10.88       106.75       100.01        35.93        22.09        26.17 
TCGA-G4-6628 TCGA-5M-AAT4 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 
       79.69         1.61        43.43        42.90        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 
       37.02        32.75        31.63        22.09        22.06         8.38 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       24.39        20.12        19.66        16.24        24.92        56.25 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
        3.02         1.02        35.01        63.98         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       19.07         0.00        29.95        61.02         6.97        54.02 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3819 
       47.05        47.01        11.01         5.03        26.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 
        1.02        17.98        15.95        38.99         0.00         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 
       33.07         0.00        36.03        53.00        18.05        31.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-A00A 
       33.01         2.01        21.99        34.06        25.02        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       17.03        34.98        10.98        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       35.01         1.02         1.02        26.01        37.02        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
        5.03         0.92        22.03        18.05        12.16        83.24 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 
        0.46         0.92        14.50        27.09         0.20        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 
       17.85        19.33        58.39         5.65        32.94        88.21 
TCGA-AZ-6599 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        6.77         3.19        12.46        12.39        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       12.76        10.06        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.99        21.14        82.95       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
       25.02        26.04        27.02        15.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 
       21.99        14.04        12.95        13.05        12.03        45.40 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       20.19        20.42        16.14        15.58        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.64        13.35        24.43        38.20        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H 
       44.32       135.65       139.17        81.37        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6302 
       47.87         1.55        34.42        13.25        35.31        67.30 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        26.04        13.78 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 
       10.98        19.33         9.93        12.79        32.98         8.42 
TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 
       31.30        11.90        70.03 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.53               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            148.01             140.38 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             22.03              22.06 
[1] "0.5 - 148.0 (22.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  13Q GAIN MUTATED        41        0       15        62         3         1
  13Q GAIN WILD-TYPE      33        1       14        70         7         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED          11          8         35         25       35
  13Q GAIN WILD-TYPE         9          0         24         16       10
                    vv
clus                 STAGE IVA STAGE IVB
  13Q GAIN MUTATED          12         0
  13Q GAIN WILD-TYPE         5         2
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  41                 33
  STAGE IA                  0                  1
  STAGE II                 15                 14
  STAGE IIA                62                 70
  STAGE IIB                 3                  7
  STAGE IIC                 1                  0
  STAGE III                11                  9
  STAGE IIIA                8                  0
  STAGE IIIB               35                 24
  STAGE IIIC               25                 16
  STAGE IV                 35                 10
  STAGE IVA                12                  5
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED     7  44 173  31
  13Q GAIN WILD-TYPE   4  33 132  24
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                7                  4
  T2               44                 33
  T3              173                132
  T4               31                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  13Q GAIN MUTATED   132  69  54
  13Q GAIN WILD-TYPE 130  36  28
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0              132                130
  N1               69                 36
  N2               54                 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"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   179  47
  13Q GAIN WILD-TYPE 149  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    179   47
  13Q GAIN WILD-TYPE  149   17
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0              179                149
  1               47                 17
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   117 138
  13Q GAIN WILD-TYPE  96  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    117  138
  13Q GAIN WILD-TYPE   96   98
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE              117                 96
  MALE                138                 98
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   220   6
  13Q GAIN WILD-TYPE 150   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    220    6
  13Q GAIN WILD-TYPE  150    3
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO               220                150
  YES                6                  3
[1] 2 2
[1] FALSE
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   236  17
  13Q GAIN WILD-TYPE 146  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    236   17
  13Q GAIN WILD-TYPE  146   45
                               clus
vv                              13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       236                146
  COLON MUCINOUS ADENOCARCINOMA               17                 45
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED   177   2  19   9
  13Q GAIN WILD-TYPE 146   2   6  16
D25V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0              177                146
  R1                2                  2
  R2               19                  6
  RX                9                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     4
  13Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                          33   127
  13Q GAIN WILD-TYPE                        26    85
D25V12, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                      33                 26
  WHITE                                         127                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     3 154
  13Q GAIN WILD-TYPE   1 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3  154
  13Q GAIN WILD-TYPE    1  115
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO              154                115
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    28   6
  14Q GAIN WILD-TYPE 307  95
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                34                402 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                 95 
$`14Q GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-6649 TCGA-DM-A285 TCGA-A6-2674 TCGA-A6-2686 TCGA-A6-5667 
       45.60        24.16         5.88        43.76        37.02        29.16 
TCGA-A6-6648 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3851 
       25.18        26.01        12.99        20.98        78.08        33.07 
TCGA-AA-3852 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A01D TCGA-AA-A02O 
        0.00        24.00         2.01        19.00        10.98         0.92 
TCGA-AD-6890 TCGA-AD-6965 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-6719 TCGA-CM-5864 
       24.53        26.47         3.19        12.69        14.30        15.02 
TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6538 TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6307 
       11.01        19.59        17.13        95.18         1.55        55.04 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5YW 
       46.75        74.79        12.79        29.46 

$`14Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        14.53         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       37.05        37.25        34.65        32.75        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       29.00        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 
       37.02         0.00        17.03        10.06         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       27.02         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R 
       51.98         2.96        39.98         2.01         5.03        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        5.79        22.42        27.42        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5256 
       12.10        29.56         5.23        11.74        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       25.48        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       26.04        13.78        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        15.65        16.80        42.77        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        38.70        60.13        11.90        70.03 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                  0 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             95.18             148.01 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            22.490             22.045 
[1] "0.0 - 95.2 (22.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  14Q GAIN MUTATED         5        0        2        10         0         0
  14Q GAIN WILD-TYPE      69        1       27       122        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           0          1          4          5        3
  14Q GAIN WILD-TYPE        20          7         55         36       42
                    vv
clus                 STAGE IVA STAGE IVB
  14Q GAIN MUTATED           3         1
  14Q GAIN WILD-TYPE        14         1
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   5                 69
  STAGE IA                  0                  1
  STAGE II                  2                 27
  STAGE IIA                10                122
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 20
  STAGE IIIA                1                  7
  STAGE IIIB                4                 55
  STAGE IIIC                5                 36
  STAGE IV                  3                 42
  STAGE IVA                 3                 14
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED     1   5  24   5
  14Q GAIN WILD-TYPE  10  72 281  50
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                1                 10
  T2                5                 72
  T3               24                281
  T4                5                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  14Q GAIN MUTATED    19   7   9
  14Q GAIN WILD-TYPE 243  98  73
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               19                243
  N1                7                 98
  N2                9                 73
[1] 3 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    23   7
  14Q GAIN WILD-TYPE 305  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     23    7
  14Q GAIN WILD-TYPE  305   57
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               23                305
  1                7                 57
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    15  20
  14Q GAIN WILD-TYPE 198 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15   20
  14Q GAIN WILD-TYPE  198  216
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               15                198
  MALE                 20                216
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    28   0
  14Q GAIN WILD-TYPE 342   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     28    0
  14Q GAIN WILD-TYPE  342    9
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                28                342
  YES                0                  9
[1] 2 2
[1] FALSE
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    26   9
  14Q GAIN WILD-TYPE 356  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     26    9
  14Q GAIN WILD-TYPE  356   53
                               clus
vv                              14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        26                356
  COLON MUCINOUS ADENOCARCINOMA                9                 53
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    23   1   1   3
  14Q GAIN WILD-TYPE 300   3  24  22
D26V10, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               23                300
  R1                1                  3
  R2                1                 24
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  1     2
  14Q GAIN WILD-TYPE                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           2    19
  14Q GAIN WILD-TYPE                        57   193
D26V12, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       2                 57
  WHITE                                          19                193
[1] 4 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     0  23
  14Q GAIN WILD-TYPE   4 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   23
  14Q GAIN WILD-TYPE    4  246
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               23                246
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     8   2
  15Q GAIN WILD-TYPE 327  99
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                426 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 99 
$`15Q GAIN MUTATED`
TCGA-A6-6649 TCGA-3L-AA1B TCGA-AA-3534 TCGA-AA-3941 TCGA-AZ-4614 TCGA-CA-5254 
       24.16        15.62        29.00        24.00         5.65        12.69 
TCGA-CM-6161 TCGA-D5-6531 TCGA-DM-A1DB TCGA-G4-6297 
       15.02        17.75        44.32        82.39 

$`15Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 
        1.02         9.07        19.07         0.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       26.47        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       19.59        56.09        55.92        20.19        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       35.31       133.18         8.35        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        38.70        60.13        11.90        70.03 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              5.65               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             82.39             148.01 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            20.875             22.045 
[1] "5.7 - 82.4 (20.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  15Q GAIN MUTATED         2        0        0         4         0         0
  15Q GAIN WILD-TYPE      72        1       29       128        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           0          0          1          0        2
  15Q GAIN WILD-TYPE        20          8         58         41       43
                    vv
clus                 STAGE IVA STAGE IVB
  15Q GAIN MUTATED           2         0
  15Q GAIN WILD-TYPE        15         2
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                 72
  STAGE IA                  0                  1
  STAGE II                  0                 29
  STAGE IIA                 4                128
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 20
  STAGE IIIA                0                  8
  STAGE IIIB                1                 58
  STAGE IIIC                0                 41
  STAGE IV                  2                 43
  STAGE IVA                 2                 15
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED     0   2   6   3
  15Q GAIN WILD-TYPE  11  75 299  52
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                0                 11
  T2                2                 75
  T3                6                299
  T4                3                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  15Q GAIN MUTATED     6   3   2
  15Q GAIN WILD-TYPE 256 102  80
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                6                256
  N1                3                102
  N2                2                 80
[1] 3 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     7   4
  15Q GAIN WILD-TYPE 321  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7    4
  15Q GAIN WILD-TYPE  321   60
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                7                321
  1                4                 60
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     8   3
  15Q GAIN WILD-TYPE 205 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8    3
  15Q GAIN WILD-TYPE  205  233
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                8                205
  MALE                  3                233
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     9   0
  15Q GAIN WILD-TYPE 361   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9    0
  15Q GAIN WILD-TYPE  361    9
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 9                361
  YES                0                  9
[1] 2 2
[1] FALSE
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    10   1
  15Q GAIN WILD-TYPE 372  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     10    1
  15Q GAIN WILD-TYPE  372   61
                               clus
vv                              15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        10                372
  COLON MUCINOUS ADENOCARCINOMA                1                 61
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     7   0   1   1
  15Q GAIN WILD-TYPE 316   4  24  24
D27V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                7                316
  R1                0                  4
  R2                1                 24
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     1
  15Q GAIN WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           1     6
  15Q GAIN WILD-TYPE                        58   206
D27V12, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 58
  WHITE                                           6                206
[1] 4 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     0   8
  15Q GAIN WILD-TYPE   4 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    8
  15Q GAIN WILD-TYPE    4  261
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                261
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    83  18
  16P GAIN WILD-TYPE 252  83
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               101                335 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                18                 83 
$`16P GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       24.33        45.60        13.02        19.99        19.99        19.00 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3976 
       14.93        24.03        29.98        12.99         2.01        26.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 
        1.94        49.08        63.62        39.45        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 
       44.91        35.11        16.57        37.25        32.45        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 
       29.19        29.16        24.13        23.87        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       12.99        33.99        24.00        50.04        47.01        15.02 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 
       36.95        37.02        17.03        33.07         0.99        17.03 
TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3982 
       27.02        24.00        20.98        34.03        16.08        27.02 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A03J 
       34.03        42.02        15.02        12.00        33.04        40.96 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L 
       22.42        27.42        26.47         0.95        33.01        17.26 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 
       18.84         5.13        62.79        29.56         5.23        12.69 
TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 
       12.59        14.30       148.01        21.99        20.02         8.02 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       13.02        22.98        32.02        17.03        14.04        29.03 
TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 
       14.99        15.02        10.06        19.59        18.25        25.48 
TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-F4-6460 
       15.12        12.49        13.41        11.38        38.20        31.96 
TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 
        1.55        82.39        65.85        44.68        55.04        39.42 
TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC TCGA-QL-A97D 
       26.43        13.78        46.75        12.79        21.90 

$`16P GAIN WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 
        0.99        17.95        23.01         6.05         0.92        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3972 
       85.05        19.04        19.04        31.07        24.00        50.99 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       12.66         1.61         9.53        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       42.28        37.05        37.02        34.65        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3555 
       19.07         0.00        29.00        14.01        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        2.01        14.01        47.05        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 
        1.02        17.98        15.95        38.99         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
        0.00         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       18.05        31.00         2.01        33.01        26.01         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       21.99        13.05        34.06        25.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
       22.03        41.00        39.98        18.05        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       24.53         5.79        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       27.09        16.31         0.20        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        88.21        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19        12.36        12.46        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.20        12.76        10.06        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 
       23.05        37.02        25.02        26.04        27.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        16.04        21.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.03        45.40        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        20.42        17.75        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 
        0.53        47.41        35.31       133.18         8.35        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 
       67.30        53.62        85.48        61.91        36.00        26.04 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        38.70        60.13        11.90        70.03 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.95               0.00 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            148.01             140.38 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             24.03              21.76 
[1] "0.9 - 148.0 (24.0)" "0.0 - 140.4 (21.8)"
[1] "hr=" "1.3"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16P GAIN MUTATED        12        1        3        25         1         0
  16P GAIN WILD-TYPE      62        0       26       107         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           7          6         13         14       13
  16P GAIN WILD-TYPE        13          2         46         27       32
                    vv
clus                 STAGE IVA STAGE IVB
  16P GAIN MUTATED           4         1
  16P GAIN WILD-TYPE        13         1
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  12                 62
  STAGE IA                  1                  0
  STAGE II                  3                 26
  STAGE IIA                25                107
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 7                 13
  STAGE IIIA                6                  2
  STAGE IIIB               13                 46
  STAGE IIIC               14                 27
  STAGE IV                 13                 32
  STAGE IVA                 4                 13
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED     3  18  73  11
  16P GAIN WILD-TYPE   8  59 232  44
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                  8
  T2               18                 59
  T3               73                232
  T4               11                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  16P GAIN MUTATED    48  32  26
  16P GAIN WILD-TYPE 214  73  56
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               48                214
  N1               32                 73
  N2               26                 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"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    72  18
  16P GAIN WILD-TYPE 256  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     72   18
  16P GAIN WILD-TYPE  256   46
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               72                256
  1               18                 46
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    50  56
  16P GAIN WILD-TYPE 163 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     50   56
  16P GAIN WILD-TYPE  163  180
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               50                163
  MALE                 56                180
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    93   2
  16P GAIN WILD-TYPE 277   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     93    2
  16P GAIN WILD-TYPE  277    7
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                93                277
  YES                2                  7
[1] 2 2
[1] FALSE
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    99   5
  16P GAIN WILD-TYPE 283  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     99    5
  16P GAIN WILD-TYPE  283   57
                               clus
vv                              16P GAIN MUTATED 16P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        99                283
  COLON MUCINOUS ADENOCARCINOMA                5                 57
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    81   1   6   5
  16P GAIN WILD-TYPE 242   3  19  20
D28V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               81                242
  R1                1                  3
  R2                6                 19
  RX                5                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  1     3
  16P GAIN WILD-TYPE                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          12    49
  16P GAIN WILD-TYPE                        47   163
D28V12, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                      12                 47
  WHITE                                          49                163
[1] 4 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  60
  16P GAIN WILD-TYPE   3 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   60
  16P GAIN WILD-TYPE    3  209
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               60                209
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    82  17
  16Q GAIN WILD-TYPE 253  84
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                99                337 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                 84 
$`16Q GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3688 TCGA-AA-3844 
       24.33        45.60        13.02        19.99        19.00        14.93 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3976 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 
       24.03        12.99        26.01         1.94        49.08        63.62 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       39.45        43.76        43.43        44.91        35.11        16.57 
TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6140 
       37.25        32.45        30.44        29.19        29.16        24.13 
TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3553 
       23.87        29.00        26.01        12.99        33.99        24.00 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       50.04        47.01        15.02        36.95        37.02        17.03 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3955 
       33.07         0.99        17.03        27.02        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C 
       34.03        16.08        27.02        34.03        42.02        15.02 
TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.00        33.04        40.96        22.42        27.42        26.47 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 
        0.95        33.01        17.26        18.84         5.13        62.79 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5914 
       29.56         5.23        12.69        12.59       148.01        21.99 
TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 
       20.02         8.02        13.02        22.98        32.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6679 TCGA-D5-5539 
       14.04        29.03        14.99        15.02        10.06        19.59 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 
       18.25        25.48        15.12        17.13        12.49        10.13 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 
       13.41        11.38        38.20        35.97         8.61        31.96 
TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6320 
        1.55        82.39        44.68        55.04        39.42        26.43 
TCGA-G4-6323 TCGA-NH-A6GC TCGA-QL-A97D 
       13.78        12.79        21.90 

$`16Q GAIN WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
        0.99        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3870 
       36.00        85.05        19.04        19.04        31.07        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       24.00         2.01        50.99        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
       75.95       106.75       100.01         5.88        28.21        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       17.85        15.62         4.80        12.66         1.61         9.53 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2686 
       46.65        43.76        42.90        42.28        37.05        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       34.65        32.75        36.53        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       14.01        21.01        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       78.08         6.97        54.02         2.01        14.01        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       38.99         0.00        10.06         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       32.05        31.07        53.00        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 
       33.01        26.01         2.01        21.99        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK 
       18.05        12.16        83.24        24.53         5.79        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 
        0.46         0.92        14.50        27.09        16.31         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 
       21.44        17.82        17.85        19.33       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
        1.41         5.65        32.94        22.36        65.00        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
       49.41         6.77        12.10        11.74         3.19        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.46        12.39        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         2.01       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       25.02        26.04        27.02        29.06        22.03        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       45.40        54.61        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       17.75        43.27        17.85         4.80        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.35        12.00        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24        95.18        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 
        0.53        47.41        35.31       133.18         8.35        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       67.30        65.85        53.62        85.48        61.91        36.00 
TCGA-G4-6322 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.04        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        38.70        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.95               0.00 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            148.01             140.38 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             24.00              21.99 
[1] "0.9 - 148.0 (24.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16Q GAIN MUTATED        12        1        3        23         1         0
  16Q GAIN WILD-TYPE      62        0       26       109         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           7          7         16         12       11
  16Q GAIN WILD-TYPE        13          1         43         29       34
                    vv
clus                 STAGE IVA STAGE IVB
  16Q GAIN MUTATED           4         1
  16Q GAIN WILD-TYPE        13         1
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  12                 62
  STAGE IA                  1                  0
  STAGE II                  3                 26
  STAGE IIA                23                109
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 7                 13
  STAGE IIIA                7                  1
  STAGE IIIB               16                 43
  STAGE IIIC               12                 29
  STAGE IV                 11                 34
  STAGE IVA                 4                 13
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED     3  18  71  11
  16Q GAIN WILD-TYPE   8  59 234  44
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                3                  8
  T2               18                 59
  T3               71                234
  T4               11                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  16Q GAIN MUTATED    46  33  25
  16Q GAIN WILD-TYPE 216  72  57
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               46                216
  N1               33                 72
  N2               25                 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"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    72  16
  16Q GAIN WILD-TYPE 256  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     72   16
  16Q GAIN WILD-TYPE  256   48
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               72                256
  1               16                 48
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    50  54
  16Q GAIN WILD-TYPE 163 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     50   54
  16Q GAIN WILD-TYPE  163  182
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               50                163
  MALE                 54                182
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    92   2
  16Q GAIN WILD-TYPE 278   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     92    2
  16Q GAIN WILD-TYPE  278    7
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                92                278
  YES                2                  7
[1] 2 2
[1] FALSE
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    97   5
  16Q GAIN WILD-TYPE 285  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     97    5
  16Q GAIN WILD-TYPE  285   57
                               clus
vv                              16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        97                285
  COLON MUCINOUS ADENOCARCINOMA                5                 57
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    79   1   6   4
  16Q GAIN WILD-TYPE 244   3  19  21
D29V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               79                244
  R1                1                  3
  R2                6                 19
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  1     2
  16Q GAIN WILD-TYPE                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          12    51
  16Q GAIN WILD-TYPE                        47   161
D29V12, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      12                 47
  WHITE                                          51                161
[1] 4 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  61
  16Q GAIN WILD-TYPE   3 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   61
  16Q GAIN WILD-TYPE    3  208
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               61                208
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    27   2
  17P GAIN WILD-TYPE 308  99
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                29                407 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 99 
$`17P GAIN MUTATED`
TCGA-AA-3506 TCGA-AA-3939 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2686 
       58.03        12.99        15.62         4.80        12.66        37.02 
TCGA-A6-3810 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6652 TCGA-AA-3812 TCGA-AA-3821 
       36.53        29.19        25.08        24.69        35.05         1.02 
TCGA-AA-3846 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3975 TCGA-CA-6715 TCGA-CK-4948 
       17.03         2.01        13.05        34.06        12.59       148.01 
TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6929 
       22.03        14.04        11.01        15.12         4.80        13.41 
TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 TCGA-QG-A5YW 
       95.18         1.55        74.56        36.00        29.46 

$`17P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-5M-AAT4 
       35.80        26.17        91.79        79.69        17.85         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        34.65        32.75        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       29.16        27.09        22.52        24.13         8.38        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 
        5.98        37.05         5.03        26.99        10.06         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       25.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3982 
       20.98        34.03        21.99        16.08        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       26.47        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 
       47.41        35.31       133.18         8.35        82.39        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       61.91        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        16.80        42.77        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       21.90        38.70        60.13        11.90        70.03 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.02               0.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            148.01             140.38 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             17.03              22.09 
[1] "1.0 - 148.0 (17.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "3.4"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17P GAIN MUTATED         5        0        0         8         0         0
  17P GAIN WILD-TYPE      69        1       29       124        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           1          0          5          5        2
  17P GAIN WILD-TYPE        19          8         54         36       43
                    vv
clus                 STAGE IVA STAGE IVB
  17P GAIN MUTATED           3         0
  17P GAIN WILD-TYPE        14         2
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   5                 69
  STAGE IA                  0                  1
  STAGE II                  0                 29
  STAGE IIA                 8                124
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 19
  STAGE IIIA                0                  8
  STAGE IIIB                5                 54
  STAGE IIIC                5                 36
  STAGE IV                  2                 43
  STAGE IVA                 3                 14
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED     1   4  21   3
  17P GAIN WILD-TYPE  10  73 284  52
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                1                 10
  T2                4                 73
  T3               21                284
  T4                3                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  17P GAIN MUTATED    14  10   5
  17P GAIN WILD-TYPE 248  95  77
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               14                248
  N1               10                 95
  N2                5                 77
[1] 3 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    18   5
  17P GAIN WILD-TYPE 310  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     18    5
  17P GAIN WILD-TYPE  310   59
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               18                310
  1                5                 59
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    15  14
  17P GAIN WILD-TYPE 198 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     15   14
  17P GAIN WILD-TYPE  198  222
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               15                198
  MALE                 14                222
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    26   0
  17P GAIN WILD-TYPE 344   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     26    0
  17P GAIN WILD-TYPE  344    9
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                26                344
  YES                0                  9
[1] 2 2
[1] FALSE
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    24   5
  17P GAIN WILD-TYPE 358  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     24    5
  17P GAIN WILD-TYPE  358   57
                               clus
vv                              17P GAIN MUTATED 17P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        24                358
  COLON MUCINOUS ADENOCARCINOMA                5                 57
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    21   0   1   2
  17P GAIN WILD-TYPE 302   4  24  23
D30V10, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               21                302
  R1                0                  4
  R2                1                 24
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  1     1
  17P GAIN WILD-TYPE                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           6    13
  17P GAIN WILD-TYPE                        53   199
D30V12, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       6                 53
  WHITE                                          13                199
[1] 4 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     1  20
  17P GAIN WILD-TYPE   3 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   20
  17P GAIN WILD-TYPE    3  249
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               20                249
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    68  13
  17Q GAIN WILD-TYPE 267  88
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                81                355 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                13                 88 
$`17Q GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3556 TCGA-AA-3692 
       24.33        14.53         1.02        58.03        23.01        36.00 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6888 
       24.03        12.99        50.99        38.04        21.99        15.52 
TCGA-DM-A285 TCGA-G4-6310 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE 
        5.88        63.62        15.62        12.66         1.61        39.45 
TCGA-A6-2675 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 
       43.43        37.02        36.53        30.44        29.19        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-AA-3494 
       29.16        27.09        25.08        25.18        24.69         1.02 
TCGA-AA-3553 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3956 
       24.00        35.05         1.02        17.03         0.99        34.03 
TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A01G TCGA-AA-A01S 
        2.01        13.05        34.06        27.02        12.00         1.02 
TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-5407 
       41.00        24.53        27.42        16.44        16.31        88.21 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5341 
       29.56         3.19        12.59       148.01         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       22.03        17.03        14.04        29.03        21.99        14.99 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 
       13.05        11.08        11.01        19.59        55.92        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6929 TCGA-DM-A1D0 
       25.48        15.12         4.80        17.13        13.41       130.65 
TCGA-DM-A28M TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 
       95.18        74.56        65.85        55.04        39.42        36.00 
TCGA-G4-6626 TCGA-QG-A5YW TCGA-RU-A8FL 
       46.75        29.46        38.70 

$`17Q GAIN WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       45.60        13.94        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       85.05        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A024 
       24.00         2.01        26.01        24.00        19.07        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 
        1.94        49.08        28.21        23.51        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-4N-A93T 
       35.80        26.17        91.79        79.69        17.85         4.80 
TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        9.53        43.76        46.65        43.76        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       44.91        35.11        16.57        37.05        37.25        34.65 
TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       32.75        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 
       22.09        22.06        22.52        24.13         8.38        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       26.99        10.06         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       38.99        36.95        37.02         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3977 
       33.01        26.01        20.98        21.99        16.08        25.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       35.01        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        83.24         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       22.42        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
       49.41         6.77        12.10         5.23        11.74        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       13.02        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 
       15.02        15.02        15.02        12.00        16.04        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 
       10.06        12.03        45.40        54.61        56.09        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
       20.42        17.75        43.27        17.85        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6320 
       67.30        53.62        44.68        85.48        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.04        13.78        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        21.90        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.99               0.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            148.01             140.38 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             24.53              21.76 
[1] "1.0 - 148.0 (24.5)" "0.0 - 140.4 (21.8)"
[1] "hr=" "1.6"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17Q GAIN MUTATED        13        0        2        21         0         1
  17Q GAIN WILD-TYPE      61        1       27       111        10         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           3          3         13          7       11
  17Q GAIN WILD-TYPE        17          5         46         34       34
                    vv
clus                 STAGE IVA STAGE IVB
  17Q GAIN MUTATED           5         1
  17Q GAIN WILD-TYPE        12         1
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  13                 61
  STAGE IA                  0                  1
  STAGE II                  2                 27
  STAGE IIA                21                111
  STAGE IIB                 0                 10
  STAGE IIC                 1                  0
  STAGE III                 3                 17
  STAGE IIIA                3                  5
  STAGE IIIB               13                 46
  STAGE IIIC                7                 34
  STAGE IV                 11                 34
  STAGE IVA                 5                 12
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED     4  13  60   7
  17Q GAIN WILD-TYPE   7  64 245  48
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                4                  7
  T2               13                 64
  T3               60                245
  T4                7                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  17Q GAIN MUTATED    44  26  14
  17Q GAIN WILD-TYPE 218  79  68
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               44                218
  N1               26                 79
  N2               14                 68
[1] 3 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    54  17
  17Q GAIN WILD-TYPE 274  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     54   17
  17Q GAIN WILD-TYPE  274   47
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               54                274
  1               17                 47
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    39  45
  17Q GAIN WILD-TYPE 174 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     39   45
  17Q GAIN WILD-TYPE  174  191
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               39                174
  MALE                 45                191
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    71   2
  17Q GAIN WILD-TYPE 299   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     71    2
  17Q GAIN WILD-TYPE  299    7
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                71                299
  YES                2                  7
[1] 2 2
[1] FALSE
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    75   8
  17Q GAIN WILD-TYPE 307  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     75    8
  17Q GAIN WILD-TYPE  307   54
                               clus
vv                              17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        75                307
  COLON MUCINOUS ADENOCARCINOMA                8                 54
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    58   1   6   2
  17Q GAIN WILD-TYPE 265   3  19  23
D31V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               58                265
  R1                1                  3
  R2                6                 19
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     1
  17Q GAIN WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          12    45
  17Q GAIN WILD-TYPE                        47   167
D31V12, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      12                 47
  WHITE                                          45                167
[1] 4 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     3  53
  17Q GAIN WILD-TYPE   1 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3   53
  17Q GAIN WILD-TYPE    1  216
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO               53                216
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    16   6
  18P GAIN WILD-TYPE 319  95
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                22                414 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 95 
$`18P GAIN MUTATED`
TCGA-A6-6649 TCGA-DM-A285 TCGA-AA-3664 TCGA-AA-3681 TCGA-AA-3811 TCGA-AA-A01D 
       24.16         5.88        54.02         5.98        10.06        10.98 
TCGA-AA-A01Z TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-6607 TCGA-CM-4751 TCGA-CM-6171 
       37.02        12.16         0.20         3.19        27.02        14.04 
TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-6531 TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6928 
       13.05        11.08        17.75        16.14        10.13        11.64 
TCGA-DM-A1DA TCGA-DM-A28K TCGA-G4-6299 TCGA-NH-A6GA 
        7.50        98.24        74.56         9.93 

$`18P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
       49.08        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01        37.05         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E 
        1.02        33.04         1.02        26.01        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        40.96        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23        11.74        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       12.99        13.02        15.02        11.01        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       56.09        55.92        20.19        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 
       47.41        35.31       133.18         8.35        82.39        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       74.79        18.18        10.98        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        38.70        60.13        11.90        70.03 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               0.2                0.0 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             98.24             148.01 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             11.90              22.47 
[1] "0.2 - 98.2 (11.9)"  "0.0 - 148.0 (22.5)"
[1] "hr=" "1.5"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18P GAIN MUTATED         4        0        3         3         0         0
  18P GAIN WILD-TYPE      70        1       26       129        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           2          1          2          5        2
  18P GAIN WILD-TYPE        18          7         57         36       43
                    vv
clus                 STAGE IVA STAGE IVB
  18P GAIN MUTATED           0         1
  18P GAIN WILD-TYPE        17         1
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   4                 70
  STAGE IA                  0                  1
  STAGE II                  3                 26
  STAGE IIA                 3                129
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 2                 18
  STAGE IIIA                1                  7
  STAGE IIIB                2                 57
  STAGE IIIC                5                 36
  STAGE IV                  2                 43
  STAGE IVA                 0                 17
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED     0   4  16   3
  18P GAIN WILD-TYPE  11  73 289  52
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                 11
  T2                4                 73
  T3               16                289
  T4                3                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  18P GAIN MUTATED    10   4   9
  18P GAIN WILD-TYPE 252 101  73
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               10                252
  N1                4                101
  N2                9                 73
[1] 3 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    17   3
  18P GAIN WILD-TYPE 311  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     17    3
  18P GAIN WILD-TYPE  311   61
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               17                311
  1                3                 61
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     8  15
  18P GAIN WILD-TYPE 205 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8   15
  18P GAIN WILD-TYPE  205  221
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                8                205
  MALE                 15                221
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    18   0
  18P GAIN WILD-TYPE 352   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     18    0
  18P GAIN WILD-TYPE  352    9
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                18                352
  YES                0                  9
[1] 2 2
[1] FALSE
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    16   7
  18P GAIN WILD-TYPE 366  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     16    7
  18P GAIN WILD-TYPE  366   55
                               clus
vv                              18P GAIN MUTATED 18P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        16                366
  COLON MUCINOUS ADENOCARCINOMA                7                 55
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    18   0   0   0
  18P GAIN WILD-TYPE 305   4  25  25
D32V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               18                305
  R1                0                  4
  R2                0                 25
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           2    15
  18P GAIN WILD-TYPE                        57   197
D32V12, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       2                 57
  WHITE                                          15                197
[1] 4 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     0  17
  18P GAIN WILD-TYPE   4 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   17
  18P GAIN WILD-TYPE    4  252
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               17                252
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    11   2
  18Q GAIN WILD-TYPE 324  99
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                423 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 99 
$`18Q GAIN MUTATED`
TCGA-AA-3664 TCGA-AA-3681 TCGA-AA-3811 TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-6607 
       54.02         5.98        10.06        12.16         0.20         3.19 
TCGA-CM-6171 TCGA-D5-6531 TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6928 TCGA-DM-A28K 
       14.04        17.75        16.14        10.13        11.64        98.24 
TCGA-G4-6299 
       74.56 

$`18Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       17.85        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        32.75        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       78.08         6.97         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       26.47        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       19.59        56.09        55.92        20.19        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         7.53        12.39        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M 
       81.37       119.93        35.97        60.79       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       82.39        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       60.13        11.90        70.03 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               0.2                0.0 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             98.24             148.01 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             12.16              22.36 
[1] "0.2 - 98.2 (12.2)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.4"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18Q GAIN MUTATED         3        0        2         3         0         0
  18Q GAIN WILD-TYPE      71        1       27       129        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           2          1          0          2        1
  18Q GAIN WILD-TYPE        18          7         59         39       44
                    vv
clus                 STAGE IVA STAGE IVB
  18Q GAIN MUTATED           0         0
  18Q GAIN WILD-TYPE        17         2
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   3                 71
  STAGE IA                  0                  1
  STAGE II                  2                 27
  STAGE IIA                 3                129
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 2                 18
  STAGE IIIA                1                  7
  STAGE IIIB                0                 59
  STAGE IIIC                2                 39
  STAGE IV                  1                 44
  STAGE IVA                 0                 17
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED     0   3   9   2
  18Q GAIN WILD-TYPE  11  74 296  53
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                 11
  T2                3                 74
  T3                9                296
  T4                2                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  18Q GAIN MUTATED     8   2   4
  18Q GAIN WILD-TYPE 254 103  78
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                8                254
  N1                2                103
  N2                4                 78
[1] 3 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    11   1
  18Q GAIN WILD-TYPE 317  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     11    1
  18Q GAIN WILD-TYPE  317   63
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               11                317
  1                1                 63
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5   9
  18Q GAIN WILD-TYPE 208 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    9
  18Q GAIN WILD-TYPE  208  227
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                5                208
  MALE                  9                227
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    11   0
  18Q GAIN WILD-TYPE 359   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     11    0
  18Q GAIN WILD-TYPE  359    9
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                11                359
  YES                0                  9
[1] 2 2
[1] FALSE
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     9   5
  18Q GAIN WILD-TYPE 373  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      9    5
  18Q GAIN WILD-TYPE  373   57
                               clus
vv                              18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         9                373
  COLON MUCINOUS ADENOCARCINOMA                5                 57
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    12   0   0   0
  18Q GAIN WILD-TYPE 311   4  25  25
D33V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               12                311
  R1                0                  4
  R2                0                 25
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           0    10
  18Q GAIN WILD-TYPE                        59   202
D33V12, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 59
  WHITE                                          10                202
[1] 4 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     0  10
  18Q GAIN WILD-TYPE   4 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   10
  18Q GAIN WILD-TYPE    4  259
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               10                259
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    56  13
  19P GAIN WILD-TYPE 279  88
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                69                367 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                13                 88 
$`19P GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3972 TCGA-AA-A00Z TCGA-G4-6310 TCGA-NH-A8F7 
       45.60        14.53        50.99        21.99        63.62        17.85 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-2686 
       15.62        12.66        43.76        43.43        16.57        37.02 
TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 
       36.53        31.63        29.16        25.18        21.76        23.87 
TCGA-A6-A56B TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3858 TCGA-AA-3973 
       56.25        37.05        35.05         0.99        31.07        13.05 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A029 TCGA-AA-A02O 
       27.02        13.94        18.05        42.02        51.98         0.92 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-A8YK TCGA-AZ-5407 
        5.79        22.42        26.47        16.44        18.84        88.21 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 
       29.56        11.74        12.36        14.30        85.45        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 
        2.01        25.02        13.02        29.06        32.02         5.03 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6169 
       15.02        15.02        14.04        29.03        21.99        13.02 
TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6932 TCGA-DM-A0X9 
       11.08        19.59        56.09        15.12        11.38       119.70 
TCGA-DM-A28F TCGA-F4-6459 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6311 TCGA-G4-6320 
       35.97         8.61        82.39        74.56        39.42        26.43 
TCGA-G4-6627 TCGA-QG-A5YW TCGA-QL-A97D 
       74.79        29.46        21.90 

$`19P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       24.00         2.01        26.01        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
      106.75       100.01         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       23.51        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
       79.69         4.80         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 
       43.76        42.90        42.28        44.91        35.11        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       37.25        34.65        32.75        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 
       27.09        22.52        24.13         8.38        25.08        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       10.06        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
       33.07         0.00        36.03        32.05         0.99        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00A 
       16.08        34.06        25.02        27.02         7.96        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R 
       37.02         2.96        39.98         2.01         5.03        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       24.53        27.42         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        17.85        19.33       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       49.41         6.77        12.10         5.23         3.19        12.69 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       10.06        17.56       148.01        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       26.04         8.02        27.02        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 
       15.02        15.02        17.03        12.00        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 
      119.93        60.79       117.07        98.24        95.18        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 
       47.41        35.31       133.18         8.35        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.04        13.78        46.75        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        38.70        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.92               0.00 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            119.70             148.01 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             23.87              22.03 
[1] "0.9 - 119.7 (23.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19P GAIN MUTATED        10        0        4        23         0         0
  19P GAIN WILD-TYPE      64        1       25       109        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           3          2         14          4        7
  19P GAIN WILD-TYPE        17          6         45         37       38
                    vv
clus                 STAGE IVA STAGE IVB
  19P GAIN MUTATED           4         0
  19P GAIN WILD-TYPE        13         2
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  10                 64
  STAGE IA                  0                  1
  STAGE II                  4                 25
  STAGE IIA                23                109
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 3                 17
  STAGE IIIA                2                  6
  STAGE IIIB               14                 45
  STAGE IIIC                4                 37
  STAGE IV                  7                 38
  STAGE IVA                 4                 13
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED     2  10  54   7
  19P GAIN WILD-TYPE   9  67 251  48
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                2                  9
  T2               10                 67
  T3               54                251
  T4                7                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  19P GAIN MUTATED    40  23  10
  19P GAIN WILD-TYPE 222  82  72
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               40                222
  N1               23                 82
  N2               10                 72
[1] 3 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    46  11
  19P GAIN WILD-TYPE 282  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     46   11
  19P GAIN WILD-TYPE  282   53
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               46                282
  1               11                 53
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    28  45
  19P GAIN WILD-TYPE 185 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     28   45
  19P GAIN WILD-TYPE  185  191
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               28                185
  MALE                 45                191
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    60   3
  19P GAIN WILD-TYPE 310   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     60    3
  19P GAIN WILD-TYPE  310    6
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                60                310
  YES                3                  6
[1] 2 2
[1] FALSE
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    65   8
  19P GAIN WILD-TYPE 317  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     65    8
  19P GAIN WILD-TYPE  317   54
                               clus
vv                              19P GAIN MUTATED 19P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        65                317
  COLON MUCINOUS ADENOCARCINOMA                8                 54
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    51   2   2   6
  19P GAIN WILD-TYPE 272   2  23  19
D34V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               51                272
  R1                2                  2
  R2                2                 23
  RX                6                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     2
  19P GAIN WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                          12    43
  19P GAIN WILD-TYPE                        47   169
D34V12, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      12                 47
  WHITE                                          43                169
[1] 4 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     0  54
  19P GAIN WILD-TYPE   4 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   54
  19P GAIN WILD-TYPE    4  215
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               54                215
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    65  16
  19Q GAIN WILD-TYPE 270  85
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                81                355 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                16                 85 
$`19Q GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3939 TCGA-AA-3972 TCGA-G4-6310 
       45.60        14.53        58.03        12.99        50.99        63.62 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 
       17.85        15.62        12.66        39.45        43.76        43.43 
TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 
       16.57        37.02        36.53        31.63        29.16        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3502 
       25.18        21.76        23.87        61.84        56.25        35.01 
TCGA-AA-3529 TCGA-AA-3542 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3854 TCGA-AA-3973 
        0.00        12.99        35.05         0.99        36.03        13.05 
TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01G TCGA-AA-A029 TCGA-AA-A02F 
       18.05        27.02        42.02        12.00        51.98        39.98 
TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-6196 
        0.92         5.79        22.42        26.47        16.44         0.20 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 
       17.85        18.84        88.21        29.56        11.74        12.36 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4747 
       14.30        85.45        21.99         2.01        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 
       13.02        29.06        32.02         5.03        15.02        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6535 
       14.04        29.03        21.99        11.08        19.59        15.12 
TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A28F 
        4.80        11.64        12.00        11.38       119.70        35.97 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6311 TCGA-G4-6320 
        8.61        35.74        47.41        82.39        39.42        26.43 
TCGA-G4-6627 TCGA-QG-A5YW TCGA-QL-A97D 
       74.79        29.46        21.90 

$`19Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        13.94        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        4.80         1.61         9.53        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       42.28        44.91        35.11        37.05        37.25        34.65 
TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        32.45        32.91        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       24.13         8.38        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 
       19.66        20.28        16.24        24.92         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        37.05        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 
        1.02        38.99         1.02         9.07        19.07        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       29.00        26.01        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       10.06        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       16.08        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
        4.01         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W 
       37.02         2.96         2.01         5.03        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        33.01        21.44        17.82        17.26        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        62.79        49.41         6.77        12.10 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        5.23         3.19        12.69        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        17.56       148.01 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 
       23.05        20.02        26.04         8.02        27.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       22.98        30.08        15.02        15.02        17.03        12.00 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       20.42        17.75        18.25        25.48        43.27        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       13.35        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        60.79       117.07        98.24        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       31.96        11.11        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       35.31       133.18         8.35        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.04        13.78        46.75        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        38.70        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  0 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            119.70             148.01 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             23.87              22.03 
[1] "0.0 - 119.7 (23.9)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19Q GAIN MUTATED        13        0        3        26         0         0
  19Q GAIN WILD-TYPE      61        1       26       106        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           2          2         14          8        9
  19Q GAIN WILD-TYPE        18          6         45         33       36
                    vv
clus                 STAGE IVA STAGE IVB
  19Q GAIN MUTATED           5         0
  19Q GAIN WILD-TYPE        12         2
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  13                 61
  STAGE IA                  0                  1
  STAGE II                  3                 26
  STAGE IIA                26                106
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 2                 18
  STAGE IIIA                2                  6
  STAGE IIIB               14                 45
  STAGE IIIC                8                 33
  STAGE IV                  9                 36
  STAGE IVA                 5                 12
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED     2  13  61   8
  19Q GAIN WILD-TYPE   9  64 244  47
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                2                  9
  T2               13                 64
  T3               61                244
  T4                8                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  19Q GAIN MUTATED    45  26  13
  19Q GAIN WILD-TYPE 217  79  69
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               45                217
  N1               26                 79
  N2               13                 69
[1] 3 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    52  14
  19Q GAIN WILD-TYPE 276  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     52   14
  19Q GAIN WILD-TYPE  276   50
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               52                276
  1               14                 50
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    35  49
  19Q GAIN WILD-TYPE 178 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     35   49
  19Q GAIN WILD-TYPE  178  187
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               35                178
  MALE                 49                187
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    70   3
  19Q GAIN WILD-TYPE 300   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     70    3
  19Q GAIN WILD-TYPE  300    6
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                70                300
  YES                3                  6
[1] 2 2
[1] FALSE
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    72  12
  19Q GAIN WILD-TYPE 310  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     72   12
  19Q GAIN WILD-TYPE  310   50
                               clus
vv                              19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        72                310
  COLON MUCINOUS ADENOCARCINOMA               12                 50
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    59   2   3   6
  19Q GAIN WILD-TYPE 264   2  22  19
D35V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               59                264
  R1                2                  2
  R2                3                 22
  RX                6                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     2
  19Q GAIN WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                          15    48
  19Q GAIN WILD-TYPE                        44   164
D35V12, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      15                 44
  WHITE                                          48                164
[1] 4 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     1  60
  19Q GAIN WILD-TYPE   3 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   60
  19Q GAIN WILD-TYPE    3  209
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               60                209
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   178  57
  20P GAIN WILD-TYPE 157  44
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               235                201 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                57                 44 
$`20P GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 
       19.99         6.05        19.00        36.00        85.05        14.93 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       12.99        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 
       21.99        21.37        15.52        25.08       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 
       49.08         5.88        28.21        63.62        35.93        91.79 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       15.62         4.80        39.45        43.76        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        35.11        16.57        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6137 
       36.53        32.45        30.44        29.19        23.61        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       61.84         9.63         5.03         7.04         1.02        37.05 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        6.97         1.02         0.00        29.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3667 
       14.01        21.01        20.98        13.94         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       50.04        47.05        15.02        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
       35.05         0.99        25.02        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03        10.06        33.07         0.99        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       27.02        18.05        24.00        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       16.08        13.05        27.02         7.96        13.94        19.00 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01D 
       18.05         4.01        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       32.02        12.00        31.00        31.00        33.04        26.01 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.96         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       39.98        12.16        24.53         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       16.44         0.46        14.50        16.31         0.95        33.01 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 
       17.26        17.85        19.33        18.84         1.41         5.13 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        49.41        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.46        12.59        12.59 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-4744 TCGA-CM-4747 
       14.30        17.56       148.01        85.45        20.02        25.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 
        8.02        13.02        29.06        22.98         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       14.99        13.02        14.04        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6531 
       11.01        45.40        54.61        19.59        20.19        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6922 
       18.25        25.48        17.85        12.49        12.39        10.13 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04        11.64        13.41        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
       24.43        38.20       130.65        13.32        12.59         7.50 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
      139.17        14.04       119.93        35.97       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 
        8.61        31.96        35.74         6.18         1.55        41.42 
TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6311 
       33.67        47.41       133.18        82.39        55.04        39.42 
TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       61.91        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QL-A97D 
       21.90 

$`20P GAIN WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 
       19.99         0.92        19.04        19.04        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4313 
       29.98        24.00         2.01        39.06        10.88        75.95 
TCGA-AZ-6601 TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
      100.01        23.51        22.09        35.80        26.17        79.69 
TCGA-NH-A8F7 TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       17.85        12.66         1.61         9.53        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       42.28        37.05        32.75        32.91        31.63        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        29.16        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        20.61        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3517 
       24.92        56.25         3.02        35.01        63.98        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3553 
        1.02         9.07        19.07        26.01        33.99        24.00 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3678 
       29.95        61.02        78.08         6.97        54.02        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       11.01         5.98        26.99         1.02        17.98        15.95 
TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
       36.95         0.00         0.00        36.03        32.05        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3975 
       31.00         2.01        33.01        26.01         2.01        34.06 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       25.02        27.02        38.04        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01P 
       27.02        42.02         0.99        34.98        15.02        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A02F 
        1.02        35.01         1.02         1.02        37.02        39.98 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6965 TCGA-AM-5821 
       22.03        18.05        40.96        83.24        26.47         0.92 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4315 
       27.09         0.20        21.44        17.82       109.28        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6606 
        5.65        32.94        22.36        88.21         6.77        11.74 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 
       12.39        12.20        12.76        10.06        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 
       23.05        37.02        26.04        27.02        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6170 
       32.02        15.02        12.00        29.03        12.99        15.02 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 
       12.95        13.05        10.06        12.03        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       20.42        43.27        15.12         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 
       15.58         7.53        12.43        14.30         9.44        13.35 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       12.00        92.75        49.91       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K 
      135.65         7.76        26.47        81.37        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
       11.11        35.74        47.87        34.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        0.53        35.31         8.35        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50U 
       53.62        44.68        85.48        36.00        26.43        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       19.33        19.33         9.93         8.42        31.30        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       60.13        11.90        70.03 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 0                  0 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            148.01             140.38 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             19.99              24.39 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (24.4)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20P GAIN MUTATED        41        1       14        62         3         0
  20P GAIN WILD-TYPE      33        0       15        70         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           9          8         28         22       33
  20P GAIN WILD-TYPE        11          0         31         19       12
                    vv
clus                 STAGE IVA STAGE IVB
  20P GAIN MUTATED          13         1
  20P GAIN WILD-TYPE         4         1
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  41                 33
  STAGE IA                  1                  0
  STAGE II                 14                 15
  STAGE IIA                62                 70
  STAGE IIB                 3                  7
  STAGE IIC                 0                  1
  STAGE III                 9                 11
  STAGE IIIA                8                  0
  STAGE IIIB               28                 31
  STAGE IIIC               22                 19
  STAGE IV                 33                 12
  STAGE IVA                13                  4
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P GAIN MUTATED     7  44 163  27
  20P GAIN WILD-TYPE   4  33 142  28
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                7                  4
  T2               44                 33
  T3              163                142
  T4               27                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  20P GAIN MUTATED   130  63  49
  20P GAIN WILD-TYPE 132  42  33
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              130                132
  N1               63                 42
  N2               49                 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"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   167  47
  20P GAIN WILD-TYPE 161  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    167   47
  20P GAIN WILD-TYPE  161   17
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              167                161
  1               47                 17
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   108 134
  20P GAIN WILD-TYPE 105 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    108  134
  20P GAIN WILD-TYPE  105  102
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE              108                105
  MALE                134                102
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   199   6
  20P GAIN WILD-TYPE 171   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    199    6
  20P GAIN WILD-TYPE  171    3
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               199                171
  YES                6                  3
[1] 2 2
[1] FALSE
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   218  20
  20P GAIN WILD-TYPE 164  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    218   20
  20P GAIN WILD-TYPE  164   42
                               clus
vv                              20P GAIN MUTATED 20P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       218                164
  COLON MUCINOUS ADENOCARCINOMA               20                 42
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED   170   2  18  10
  20P GAIN WILD-TYPE 153   2   7  15
D36V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              170                153
  R1                2                  2
  R2               18                  7
  RX               10                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  1     6
  20P GAIN WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          30   114
  20P GAIN WILD-TYPE                        29    98
D36V12, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           6                  5
  BLACK OR AFRICAN AMERICAN                      30                 29
  WHITE                                         114                 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"
D36V13, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1 142
  20P GAIN WILD-TYPE   3 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1  142
  20P GAIN WILD-TYPE    3  127
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO              142                127
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   241  69
  20Q GAIN WILD-TYPE  94  32
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               310                126 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                69                 32 
$`20Q GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       14.93        31.07        24.03        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       25.08       106.75         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B 
       23.51        63.62        35.93        91.79        17.85        15.62 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
        4.80         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        35.11        16.57        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.45        32.91        30.44        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 
       32.71        29.16        27.09        22.52        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        20.61        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       61.84        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 
       37.05         6.97         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 
       33.99        21.01        24.00        20.98        13.94        78.08 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        10.06        35.05         0.99        25.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       33.07        32.05         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       18.05        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       16.08        13.05        34.06        27.02         7.96        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       12.00        31.00        31.00         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 
        0.92        41.00        39.98        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L 
       14.50        16.31         0.95        33.01         0.20        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 
       17.85        19.33        18.84       109.28         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        62.79        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
        5.23         3.19        12.69        12.36        12.46        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.59        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       21.99         2.01        20.02        37.02        25.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        11.08        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        12.49         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 
       12.43        14.30         9.04        11.64        13.41        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 
       49.91        13.32        12.59         7.50        44.32       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
       14.04        26.47       119.93        35.97       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
        8.61        31.96        35.74        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 
       47.41       133.18         8.35        82.39        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        55.04        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB 
       26.04        13.78        46.75        74.79        18.18        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       21.90        38.70        60.13        11.90 

$`20Q GAIN WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
        0.92        19.04        19.04        29.98        24.00         2.01 
TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 
       39.06        10.88        75.95       100.01        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       26.17        79.69        12.66         9.53        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 
       42.28        37.05        32.75        31.63        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       22.06         8.38        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 
       24.92         3.02        35.01        63.98         1.02        29.95 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 
       61.02         6.97        54.02        11.01         5.98        26.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
        1.02        17.98        15.95         0.00         0.00        36.03 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 
       53.00        31.00         2.01        33.01        26.01        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 
       27.02        38.04        30.02        18.05         0.99        34.98 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A02R TCGA-AA-A03F 
       38.07         1.02        35.01         1.02        22.03        18.05 
TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       83.24         0.92        27.09        21.44        17.82        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5796 
        5.65        32.94        88.21         6.77        11.74        12.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       12.76        10.06        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 
       82.95       124.27        23.05        26.04        27.02        15.02 
TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 
       12.00        12.99        12.95        13.05        12.03        20.42 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 
       16.14        15.58         9.44        13.35        12.00       140.38 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K 
      131.51       135.65         7.76        81.37        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       11.11        47.87        35.31        67.30        53.62        85.48 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 
       10.98        19.33        19.33         9.93        31.30        70.03 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  0 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            148.01             140.38 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             21.99              22.09 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1"  
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20Q GAIN MUTATED        53        1       17        85         4         1
  20Q GAIN WILD-TYPE      21        0       12        47         6         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED          13          8         42         32       39
  20Q GAIN WILD-TYPE         7          0         17          9        6
                    vv
clus                 STAGE IVA STAGE IVB
  20Q GAIN MUTATED          15         1
  20Q GAIN WILD-TYPE         2         1
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  53                 21
  STAGE IA                  1                  0
  STAGE II                 17                 12
  STAGE IIA                85                 47
  STAGE IIB                 4                  6
  STAGE IIC                 1                  0
  STAGE III                13                  7
  STAGE IIIA                8                  0
  STAGE IIIB               42                 17
  STAGE IIIC               32                  9
  STAGE IV                 39                  6
  STAGE IVA                15                  2
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q GAIN MUTATED     7  58 220  33
  20Q GAIN WILD-TYPE   4  19  85  22
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                7                  4
  T2               58                 19
  T3              220                 85
  T4               33                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  20Q GAIN MUTATED   173  84  62
  20Q GAIN WILD-TYPE  89  21  20
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              173                 89
  N1               84                 21
  N2               62                 20
[1] 3 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   225  55
  20Q GAIN WILD-TYPE 103   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    225   55
  20Q GAIN WILD-TYPE  103    9
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              225                103
  1               55                  9
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   145 174
  20Q GAIN WILD-TYPE  68  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    145  174
  20Q GAIN WILD-TYPE   68   62
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              145                 68
  MALE                174                 62
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   265   7
  20Q GAIN WILD-TYPE 105   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    265    7
  20Q GAIN WILD-TYPE  105    2
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               265                105
  YES                7                  2
[1] 2 2
[1] FALSE
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   289  26
  20Q GAIN WILD-TYPE  93  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    289   26
  20Q GAIN WILD-TYPE   93   36
                               clus
vv                              20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       289                 93
  COLON MUCINOUS ADENOCARCINOMA               26                 36
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   228   3  21  14
  20Q GAIN WILD-TYPE  95   1   4  11
D37V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              228                 95
  R1                3                  1
  R2               21                  4
  RX               14                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  1     7
  20Q GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          40   155
  20Q GAIN WILD-TYPE                        19    57
D37V12, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           7                  4
  BLACK OR AFRICAN AMERICAN                      40                 19
  WHITE                                         155                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3 192
  20Q GAIN WILD-TYPE   1  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  192
  20Q GAIN WILD-TYPE    1   77
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO              192                 77
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    17   6
  21Q GAIN WILD-TYPE 318  95
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                23                413 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 95 
$`21Q GAIN MUTATED`
TCGA-AZ-6608 TCGA-DM-A285 TCGA-4T-AA8H TCGA-A6-5662 TCGA-AA-3553 TCGA-AA-3666 
        1.94         5.88        12.66        23.61        24.00         2.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AY-4071 TCGA-AZ-5407 TCGA-CA-5255 TCGA-CM-5868 
       50.04        47.01         0.95        88.21        12.36        17.03 
TCGA-D5-5539 TCGA-D5-6898 TCGA-D5-6932 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M 
       19.59         7.53        11.38        14.04        35.97        95.18 
TCGA-G4-6297 TCGA-NH-A50V TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL 
       82.39        19.33        29.46        21.90        38.70 

$`21Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
       49.08        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
        4.80         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 
       61.02        78.08         6.97        54.02        14.01        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09        16.31        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       54.61        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        9.93        15.65        12.79        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        60.13        11.90        70.03 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.95               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             95.18             148.01 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             19.59              22.09 
[1] "0.9 - 95.2 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  21Q GAIN MUTATED         6        0        1         4         0         0
  21Q GAIN WILD-TYPE      68        1       28       128        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           2          2          3          2        2
  21Q GAIN WILD-TYPE        18          6         56         39       43
                    vv
clus                 STAGE IVA STAGE IVB
  21Q GAIN MUTATED           2         0
  21Q GAIN WILD-TYPE        15         2
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   6                 68
  STAGE IA                  0                  1
  STAGE II                  1                 28
  STAGE IIA                 4                128
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 2                 18
  STAGE IIIA                2                  6
  STAGE IIIB                3                 56
  STAGE IIIC                2                 39
  STAGE IV                  2                 43
  STAGE IVA                 2                 15
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED     2   6  15   1
  21Q GAIN WILD-TYPE   9  71 290  54
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                2                  9
  T2                6                 71
  T3               15                290
  T4                1                 54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  21Q GAIN MUTATED    11   6   7
  21Q GAIN WILD-TYPE 251  99  75
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               11                251
  N1                6                 99
  N2                7                 75
[1] 3 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    14   4
  21Q GAIN WILD-TYPE 314  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     14    4
  21Q GAIN WILD-TYPE  314   60
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               14                314
  1                4                 60
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    13  11
  21Q GAIN WILD-TYPE 200 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     13   11
  21Q GAIN WILD-TYPE  200  225
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               13                200
  MALE                 11                225
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    17   1
  21Q GAIN WILD-TYPE 353   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     17    1
  21Q GAIN WILD-TYPE  353    8
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                17                353
  YES                1                  8
[1] 2 2
[1] FALSE
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    18   5
  21Q GAIN WILD-TYPE 364  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     18    5
  21Q GAIN WILD-TYPE  364   57
                               clus
vv                              21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        18                364
  COLON MUCINOUS ADENOCARCINOMA                5                 57
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    14   0   0   2
  21Q GAIN WILD-TYPE 309   4  25  23
D38V10, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               14                309
  R1                0                  4
  R2                0                 25
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     1
  21Q GAIN WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           5    14
  21Q GAIN WILD-TYPE                        54   198
D38V12, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       5                 54
  WHITE                                          14                198
[1] 4 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     0  19
  21Q GAIN WILD-TYPE   4 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   19
  21Q GAIN WILD-TYPE    4  250
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               19                250
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    10   2
  22Q GAIN WILD-TYPE 325  99
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                12                424 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 99 
$`22Q GAIN MUTATED`
TCGA-AA-3715 TCGA-G4-6314 TCGA-A6-4107 TCGA-A6-6140 TCGA-AA-3494 TCGA-AA-3553 
       19.04        35.93        32.45        24.13         1.02        24.00 
TCGA-AA-A02E TCGA-CK-4948 TCGA-CM-6163 TCGA-CM-6676 TCGA-CM-6679 TCGA-RU-A8FL 
        2.96       148.01        14.04        11.08        10.06        38.70 

$`22Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 
       49.08         5.88        28.21        23.51        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       27.09        22.52         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        5.03         7.04         3.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       18.84       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       21.90        60.13        11.90        70.03 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.02               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            148.01             140.38 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            21.520             22.045 
[1] "1.0 - 148.0 (21.5)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.3"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  22Q GAIN MUTATED         3        0        1         2         0         0
  22Q GAIN WILD-TYPE      71        1       28       130        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           1          0          2          0        3
  22Q GAIN WILD-TYPE        19          8         57         41       42
                    vv
clus                 STAGE IVA STAGE IVB
  22Q GAIN MUTATED           0         0
  22Q GAIN WILD-TYPE        17         2
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   3                 71
  STAGE IA                  0                  1
  STAGE II                  1                 28
  STAGE IIA                 2                130
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 19
  STAGE IIIA                0                  8
  STAGE IIIB                2                 57
  STAGE IIIC                0                 41
  STAGE IV                  3                 42
  STAGE IVA                 0                 17
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED     1   2   9   0
  22Q GAIN WILD-TYPE  10  75 296  55
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                1                 10
  T2                2                 75
  T3                9                296
  T4                0                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  22Q GAIN MUTATED     7   3   2
  22Q GAIN WILD-TYPE 255 102  80
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                7                255
  N1                3                102
  N2                2                 80
[1] 3 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     8   3
  22Q GAIN WILD-TYPE 320  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      8    3
  22Q GAIN WILD-TYPE  320   61
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                8                320
  1                3                 61
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     5   7
  22Q GAIN WILD-TYPE 208 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5    7
  22Q GAIN WILD-TYPE  208  229
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                5                208
  MALE                  7                229
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    10   0
  22Q GAIN WILD-TYPE 360   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10    0
  22Q GAIN WILD-TYPE  360    9
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                10                360
  YES                0                  9
[1] 2 2
[1] FALSE
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    12   0
  22Q GAIN WILD-TYPE 370  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     12    0
  22Q GAIN WILD-TYPE  370   62
                               clus
vv                              22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        12                370
  COLON MUCINOUS ADENOCARCINOMA                0                 62
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED     9   0   2   0
  22Q GAIN WILD-TYPE 314   4  23  25
D39V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                9                314
  R1                0                  4
  R2                2                 23
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           1     7
  22Q GAIN WILD-TYPE                        58   205
D39V12, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 58
  WHITE                                           7                205
[1] 4 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   8
  22Q GAIN WILD-TYPE   4 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    8
  22Q GAIN WILD-TYPE    4  261
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                261
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    52  14
  XP GAIN WILD-TYPE 283  87
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               66               370 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               14                87 
$`XP GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3524 TCGA-AA-3844 TCGA-AD-6888 TCGA-AZ-6608 TCGA-G4-6310 
       45.60        36.03        14.93        15.52         1.94        63.62 
TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 
       12.66        44.91        35.11        25.08        20.61        24.69 
TCGA-A6-6654 TCGA-AA-3534 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3664 TCGA-AA-3667 
       23.87        29.00        24.00        20.98        54.02        14.01 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3852 
       47.01         5.98         5.03        35.05         0.99         0.00 
TCGA-AA-3869 TCGA-AA-3966 TCGA-AA-3994 TCGA-AA-A01I TCGA-AA-A029 TCGA-AA-A02H 
       27.02         2.01        27.02        31.00        51.98         2.01 
TCGA-AA-A02O TCGA-AA-A02Y TCGA-AD-A5EK TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L 
        0.92        39.98        16.44        33.01         0.20        17.26 
TCGA-AY-A8YK TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 
       18.84        22.36        49.41        14.30        21.99         2.01 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5539 
       32.02         5.03        15.02        21.99        14.99        19.59 
TCGA-D5-5541 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-DM-A0X9 
       55.92        15.12         4.80        17.13        12.49       119.70 
TCGA-DM-A1DA TCGA-DM-A28F TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-G4-6299 
        7.50        35.97        98.24        95.18         8.61        74.56 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-QG-A5YW TCGA-QL-A97D TCGA-SS-A7HO 
       44.68        55.04        39.42        29.46        21.90        60.13 

$`XP GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        24.03        37.05         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       21.99        39.06        21.37        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01        49.08         5.88        28.21        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       17.85        15.62         4.80         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 
       27.09        22.52        24.13         8.38        25.18        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 
       26.01        12.99        14.01        33.99        21.01        29.95 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3673 
       13.94        61.02        78.08         6.97         2.01        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3811 
       47.05        15.02        11.01        37.05        26.99        10.06 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02        27.02         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W 
       37.02         2.96        39.98         5.03        22.03        41.00 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       22.42        27.42        26.47         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       27.09        16.31         0.95        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        65.00        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 
       29.06        22.03        22.98        30.08        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00        14.04        29.03        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        54.61        56.09        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 
       18.25        25.48        43.27        17.85        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       60.79       117.07        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 
        8.35        82.39        67.30        65.85        53.62        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        16.80        42.77        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 
       31.30        38.70        11.90        70.03 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 0 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           119.70            148.01 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           22.175            22.045 
[1] "0.0 - 119.7 (22.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XP GAIN MUTATED        10        0        7        14         2         0
  XP GAIN WILD-TYPE      64        1       22       118         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           3          2         12          6        4
  XP GAIN WILD-TYPE        17          6         47         35       41
                   vv
clus                STAGE IVA STAGE IVB
  XP GAIN MUTATED           6         0
  XP GAIN WILD-TYPE        11         2
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 10                64
  STAGE IA                 0                 1
  STAGE II                 7                22
  STAGE IIA               14               118
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                3                17
  STAGE IIIA               2                 6
  STAGE IIIB              12                47
  STAGE IIIC               6                35
  STAGE IV                 4                41
  STAGE IVA                6                11
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP GAIN MUTATED     0  13  53   2
  XP GAIN WILD-TYPE  11  64 252  53
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               0                11
  T2              13                64
  T3              53               252
  T4               2                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  XP GAIN MUTATED    37  20  11
  XP GAIN WILD-TYPE 225  85  71
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              37               225
  N1              20                85
  N2              11                71
[1] 3 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    47  10
  XP GAIN WILD-TYPE 281  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     47   10
  XP GAIN WILD-TYPE  281   54
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              47               281
  1              10                54
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    38  30
  XP GAIN WILD-TYPE 175 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     38   30
  XP GAIN WILD-TYPE  175  206
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              38               175
  MALE                30               206
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    52   2
  XP GAIN WILD-TYPE 318   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     52    2
  XP GAIN WILD-TYPE  318    7
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               52               318
  YES               2                 7
[1] 2 2
[1] FALSE
D40V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    59   9
  XP GAIN WILD-TYPE 323  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     59    9
  XP GAIN WILD-TYPE  323   53
                               clus
vv                              XP GAIN MUTATED XP GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       59               323
  COLON MUCINOUS ADENOCARCINOMA               9                53
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    47   0   4   4
  XP GAIN WILD-TYPE 276   4  21  21
D40V10, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              47               276
  R1               0                 4
  R2               4                21
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  0     1
  XP GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                          12    32
  XP GAIN WILD-TYPE                        47   180
D40V12, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     12                47
  WHITE                                         32               180
[1] 4 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     0  43
  XP GAIN WILD-TYPE   4 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   43
  XP GAIN WILD-TYPE    4  226
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              43               226
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    56  20
  XQ GAIN WILD-TYPE 279  81
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               76               360 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               20                81 
$`XQ GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3524 TCGA-AA-3562 TCGA-AA-3844 TCGA-AD-6888 TCGA-AZ-6601 
       45.60        36.03        19.99        14.93        15.52       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2680 
        1.94         5.88        63.62        12.66        44.91        35.11 
TCGA-A6-2686 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-A56B 
       37.02        25.08        20.61        24.69        23.87        56.25 
TCGA-AA-3534 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 
       29.00        24.00        20.98        78.08        54.02        14.01 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       47.01         5.98         5.03        10.06        35.05         0.99 
TCGA-AA-3852 TCGA-AA-3869 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A01I TCGA-AA-A01T 
        0.00        27.02        27.02        13.94        31.00        33.04 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02Y TCGA-AD-A5EK TCGA-AY-6196 TCGA-AY-A54L 
       51.98         0.92        39.98        16.44         0.20        17.26 
TCGA-AY-A8YK TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6719 TCGA-CK-5914 
       18.84         5.65        22.36        49.41        14.30        21.99 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6167 
       22.98        32.02         5.03        15.02        21.99        14.99 
TCGA-CM-6675 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       13.05        19.59        15.12         4.80        17.13        12.49 
TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A28F TCGA-DM-A28K TCGA-DM-A28M 
       12.43       119.70         7.50        35.97        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 
        8.61         6.18        74.56        44.68        55.04        39.42 
TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QL-A97D TCGA-WS-AB45 
       15.65        29.46        21.90        70.03 

$`XQ GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        24.03        37.05         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 
        0.99        13.02        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       39.06        21.37        25.08        10.88        75.95       106.75 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       49.08        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       43.43        42.90        42.28        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       25.18        21.76        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3673 
       29.95        13.94        61.02         6.97         2.01        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3819 
       47.05        15.02        11.01        37.05        26.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 
        0.00        17.03        10.06         0.00        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 
       32.05         0.99        31.07        53.00        17.03        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       25.02        27.02         7.96        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E 
       35.01         1.02         1.02        26.01        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F 
       39.98         2.01         5.03        22.03        41.00        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       16.31         0.95        33.01        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       19.33       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.03        30.08        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6168 
       17.03        12.00        14.04        29.03        16.04        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       25.48        43.27        17.85        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
       13.41        13.35        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       31.96        11.11        35.74        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 
       47.41        35.31       133.18         8.35        82.39        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       65.85        53.62        85.48        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        12.79        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        38.70        60.13        11.90 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 0 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           119.70            148.01 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           21.990            22.075 
[1] "0.0 - 119.7 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XQ GAIN MUTATED        11        0        9        17         1         0
  XQ GAIN WILD-TYPE      63        1       20       115         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           6          2         13          8        3
  XQ GAIN WILD-TYPE        14          6         46         33       42
                   vv
clus                STAGE IVA STAGE IVB
  XQ GAIN MUTATED           6         1
  XQ GAIN WILD-TYPE        11         1
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 11                63
  STAGE IA                 0                 1
  STAGE II                 9                20
  STAGE IIA               17               115
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                6                14
  STAGE IIIA               2                 6
  STAGE IIIB              13                46
  STAGE IIIC               8                33
  STAGE IV                 3                42
  STAGE IVA                6                11
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED     0  14  63   2
  XQ GAIN WILD-TYPE  11  63 242  53
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               0                11
  T2              14                63
  T3              63               242
  T4               2                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  XQ GAIN MUTATED    42  21  16
  XQ GAIN WILD-TYPE 220  84  66
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              42               220
  N1              21                84
  N2              16                66
[1] 3 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    56  10
  XQ GAIN WILD-TYPE 272  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     56   10
  XQ GAIN WILD-TYPE  272   54
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              56               272
  1              10                54
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    42  37
  XQ GAIN WILD-TYPE 171 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     42   37
  XQ GAIN WILD-TYPE  171  199
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              42               171
  MALE                37               199
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    63   2
  XQ GAIN WILD-TYPE 307   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     63    2
  XQ GAIN WILD-TYPE  307    7
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               63               307
  YES               2                 7
[1] 2 2
[1] FALSE
D41V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    70   9
  XQ GAIN WILD-TYPE 312  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     70    9
  XQ GAIN WILD-TYPE  312   53
                               clus
vv                              XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       70               312
  COLON MUCINOUS ADENOCARCINOMA               9                53
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    58   0   3   4
  XQ GAIN WILD-TYPE 265   4  22  21
D41V10, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              58               265
  R1               0                 4
  R2               3                22
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     1
  XQ GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          14    37
  XQ GAIN WILD-TYPE                        45   175
D41V12, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     14                45
  WHITE                                         37               175
[1] 4 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     0  50
  XQ GAIN WILD-TYPE   4 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   50
  XQ GAIN WILD-TYPE    4  219
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              50               219
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    60  28
  1P LOSS WILD-TYPE 275  73
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               88               348 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               28                73 
$`1P LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 
       14.53        37.05        19.99        31.07        24.03        12.99 
TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 
        5.88        23.51        35.93        91.79         4.80         1.61 
TCGA-A6-2674 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6651 TCGA-AA-3488 
       43.76        29.19        23.61        22.52        21.76         5.03 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 
       38.99         9.07        50.04        37.05        10.06        38.99 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3866 TCGA-AA-3966 TCGA-AA-3968 
       37.02        10.06        33.07        17.03         2.01        21.99 
TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
        7.96        34.03        42.02        15.02        32.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 
       33.04        26.01         2.01        41.00        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 
       22.42        26.47        16.44        14.50        16.31         5.65 
TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
        5.13        12.10        29.56         5.23         3.19        12.69 
TCGA-CA-5256 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 
       12.46         2.01         8.02        13.02        22.03         5.03 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5540 
       29.03        13.02        15.02        11.08        10.06        56.09 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 
       17.75        25.48        14.30        13.41        11.38        92.75 
TCGA-DM-A1D6 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6295 
       49.91        26.47        31.96         1.55        47.41         8.35 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50U 
       82.39        65.85        61.91        36.00        46.75        10.98 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-SS-A7HO TCGA-T9-A92H 
        9.93        16.80        60.13        11.90 

$`1P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        24.03        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 
        0.99        13.02        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       14.93        29.98        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08        28.21        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 
       26.17        79.69        17.85        15.62        12.66         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       39.45        43.76        46.65        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       30.44        33.53        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       27.09        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       16.24        24.92        61.84        56.25         9.63         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         1.02        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.98         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        36.95         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02        27.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02         1.02        37.02        51.98         2.96        39.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       12.16        83.24        27.42         0.46         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        6.77        11.74        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       26.04        27.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       14.04        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       45.40        54.61        19.59        55.92        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       43.04        33.67        13.25         0.53        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        67.30        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T 
       39.42        26.43        26.04        13.78        74.79        18.18 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33        19.33        15.65        12.79        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        38.70        70.03 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1.55              0.00 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            92.75            148.01 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           20.875            22.225 
[1] "1.6 - 92.8 (20.9)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.8"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1P LOSS MUTATED         8        0        3        24         1         0
  1P LOSS WILD-TYPE      66        1       26       108         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           5          3          9         12       19
  1P LOSS WILD-TYPE        15          5         50         29       26
                   vv
clus                STAGE IVA STAGE IVB
  1P LOSS MUTATED           4         0
  1P LOSS WILD-TYPE        13         2
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  8                66
  STAGE IA                 0                 1
  STAGE II                 3                26
  STAGE IIA               24               108
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                5                15
  STAGE IIIA               3                 5
  STAGE IIIB               9                50
  STAGE IIIC              12                29
  STAGE IV                19                26
  STAGE IVA                4                13
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED     2  12  63  15
  1P LOSS WILD-TYPE   9  65 242  40
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               2                 9
  T2              12                65
  T3              63               242
  T4              15                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  1P LOSS MUTATED    41  23  28
  1P LOSS WILD-TYPE 221  82  54
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              41               221
  N1              23                82
  N2              28                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"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    58  23
  1P LOSS WILD-TYPE 270  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     58   23
  1P LOSS WILD-TYPE  270   41
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              58               270
  1              23                41
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    39  53
  1P LOSS WILD-TYPE 174 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     39   53
  1P LOSS WILD-TYPE  174  183
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              39               174
  MALE                53               183
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    80   0
  1P LOSS WILD-TYPE 290   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     80    0
  1P LOSS WILD-TYPE  290    9
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               80               290
  YES               0                 9
[1] 2 2
[1] FALSE
D42V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    83   9
  1P LOSS WILD-TYPE 299  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     83    9
  1P LOSS WILD-TYPE  299   53
                               clus
vv                              1P LOSS MUTATED 1P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       83               299
  COLON MUCINOUS ADENOCARCINOMA               9                53
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    61   2   6   4
  1P LOSS WILD-TYPE 262   2  19  21
D42V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              61               262
  R1               2                 2
  R2               6                19
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  1     2
  1P LOSS WILD-TYPE                                0     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                          14    44
  1P LOSS WILD-TYPE                        45   168
D42V12, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     14                45
  WHITE                                         44               168
[1] 4 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     2  55
  1P LOSS WILD-TYPE   2 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   55
  1P LOSS WILD-TYPE    2  214
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              55               214
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    39  13
  1Q LOSS WILD-TYPE 296  88
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               52               384 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13                88 
$`1Q LOSS MUTATED`
TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3867 TCGA-DM-A285 TCGA-G4-6625 TCGA-5M-AAT4 
       37.05        19.99        24.03         5.88        91.79         1.61 
TCGA-A6-5660 TCGA-A6-6138 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3673 TCGA-AA-3811 
       29.19        22.52        38.99         9.07        50.04        10.06 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3966 TCGA-AA-3989 TCGA-AA-A01C 
       38.99        37.02        33.07         2.01         7.96        15.02 
TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
       33.04        41.00        24.53        22.42        26.47        16.44 
TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       16.31         5.65         5.13        29.56         5.23         3.19 
TCGA-CA-5256 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6164 
       12.46         2.01         8.02        13.02        22.03        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6924 
       13.02        15.02        11.08        10.06        17.75        14.30 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A28A TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6315 
       13.41        11.38        26.47         1.55         8.35        61.91 
TCGA-G4-6317 TCGA-NH-A50U TCGA-SS-A7HO TCGA-T9-A92H 
       36.00        10.98        60.13        11.90 

$`1Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        31.07        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 
       75.95       106.75       100.01         1.94        49.08        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 
       79.69        17.85        15.62         4.80        12.66         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        32.75        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
       37.05        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        36.95         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
        1.02         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6963 
       18.05        40.96        12.16        83.24         5.79        27.42 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4682 
       18.84       109.28        58.39         1.41        32.94        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       26.04        27.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.35        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 
       44.68        55.04        85.48        39.42        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        46.75        74.79        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        38.70        70.03 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.55              0.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            91.79            148.01 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           15.665            22.995 
[1] "1.6 - 91.8 (15.7)"  "0.0 - 148.0 (23.0)"
[1] "hr=" "1.5"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1Q LOSS MUTATED         6        0        2        15         1         0
  1Q LOSS WILD-TYPE      68        1       27       117         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           3          3          2          7       10
  1Q LOSS WILD-TYPE        17          5         57         34       35
                   vv
clus                STAGE IVA STAGE IVB
  1Q LOSS MUTATED           2         0
  1Q LOSS WILD-TYPE        15         2
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  6                68
  STAGE IA                 0                 1
  STAGE II                 2                27
  STAGE IIA               15               117
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                3                17
  STAGE IIIA               3                 5
  STAGE IIIB               2                57
  STAGE IIIC               7                34
  STAGE IV                10                35
  STAGE IVA                2                15
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED     2   9  37   6
  1Q LOSS WILD-TYPE   9  68 268  49
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               2                 9
  T2               9                68
  T3              37               268
  T4               6                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  1Q LOSS MUTATED    28  12  14
  1Q LOSS WILD-TYPE 234  93  68
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              28               234
  N1              12                93
  N2              14                68
[1] 3 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    35  12
  1Q LOSS WILD-TYPE 293  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     35   12
  1Q LOSS WILD-TYPE  293   52
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              35               293
  1              12                52
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    22  32
  1Q LOSS WILD-TYPE 191 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     22   32
  1Q LOSS WILD-TYPE  191  204
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              22               191
  MALE                32               204
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    48   0
  1Q LOSS WILD-TYPE 322   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     48    0
  1Q LOSS WILD-TYPE  322    9
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               48               322
  YES               0                 9
[1] 2 2
[1] FALSE
D43V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    48   6
  1Q LOSS WILD-TYPE 334  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     48    6
  1Q LOSS WILD-TYPE  334   56
                               clus
vv                              1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       48               334
  COLON MUCINOUS ADENOCARCINOMA               6                56
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    35   2   3   2
  1Q LOSS WILD-TYPE 288   2  22  23
D43V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              35               288
  R1               2                 2
  R2               3                22
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  1     1
  1Q LOSS WILD-TYPE                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           9    27
  1Q LOSS WILD-TYPE                        50   185
D43V12, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      9                50
  WHITE                                         27               185
[1] 4 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     2  33
  1Q LOSS WILD-TYPE   2 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   33
  1Q LOSS WILD-TYPE    2  236
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              33               236
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     5   1
  2P LOSS WILD-TYPE 330 100
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6               430 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1               100 
$`2P LOSS MUTATED`
TCGA-AA-3560 TCGA-AA-3939 TCGA-AA-3511 TCGA-AA-3666 TCGA-AA-3842 TCGA-CA-5797 
       19.99        12.99         6.97         2.01        37.02        12.59 

$`2P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       37.05        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       36.95         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       54.61        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       38.70        60.13        11.90        70.03 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.01              0.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            37.02            148.01 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            12.79             22.09 
[1] "2.0 - 37.0 (12.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2P LOSS MUTATED         0        0        1         2         0         0
  2P LOSS WILD-TYPE      74        1       28       130        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           1          1          0          1        0
  2P LOSS WILD-TYPE        19          7         59         40       45
                   vv
clus                STAGE IVA STAGE IVB
  2P LOSS MUTATED           0         0
  2P LOSS WILD-TYPE        17         2
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                74
  STAGE IA                 0                 1
  STAGE II                 1                28
  STAGE IIA                2               130
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                19
  STAGE IIIA               1                 7
  STAGE IIIB               0                59
  STAGE IIIC               1                40
  STAGE IV                 0                45
  STAGE IVA                0                17
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED     0   1   4   1
  2P LOSS WILD-TYPE  11  76 301  54
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                11
  T2               1                76
  T3               4               301
  T4               1                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  2P LOSS MUTATED     3   2   1
  2P LOSS WILD-TYPE 259 103  81
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               3               259
  N1               2               103
  N2               1                81
[1] 3 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     6   0
  2P LOSS WILD-TYPE 322  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    0
  2P LOSS WILD-TYPE  322   64
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               6               322
  1               0                64
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1   5
  2P LOSS WILD-TYPE 212 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    5
  2P LOSS WILD-TYPE  212  231
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               1               212
  MALE                 5               231
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     5   0
  2P LOSS WILD-TYPE 365   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    0
  2P LOSS WILD-TYPE  365    9
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                5               365
  YES               0                 9
[1] 2 2
[1] FALSE
D44V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     6   0
  2P LOSS WILD-TYPE 376  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    0
  2P LOSS WILD-TYPE  376   62
                               clus
vv                              2P LOSS MUTATED 2P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        6               376
  COLON MUCINOUS ADENOCARCINOMA               0                62
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     6   0   0   0
  2P LOSS WILD-TYPE 317   4  25  25
D44V10, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               6               317
  R1               0                 4
  R2               0                25
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           0     0
  2P LOSS WILD-TYPE                        59   212
D44V12, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1               282 
       TCGA-A6-2677        TCGA-A6-2681        TCGA-A6-2682        TCGA-A6-4105 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6649        TCGA-AD-6548        TCGA-AD-6888        TCGA-AD-6895 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AD-6964        TCGA-AZ-4313        TCGA-AZ-4681        TCGA-AZ-6601 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285        TCGA-G4-6294 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6298        TCGA-G4-6310        TCGA-G4-6314        TCGA-G4-6321 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6628 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-NH-A8F7        TCGA-3L-AA1B        TCGA-4N-A93T        TCGA-4T-AA8H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-5M-AAT4        TCGA-5M-AAT6        TCGA-5M-AATE        TCGA-A6-2671 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2675        TCGA-A6-2676 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-2678        TCGA-A6-2679        TCGA-A6-2680        TCGA-A6-2683 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-2684        TCGA-A6-2685        TCGA-A6-2686        TCGA-A6-3807 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4107        TCGA-A6-5656 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660        TCGA-A6-5661 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665        TCGA-A6-5666 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-5667        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6140 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6141        TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6650 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6651        TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6780        TCGA-A6-6781        TCGA-A6-6782        TCGA-A6-A565 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-A566        TCGA-A6-A567        TCGA-A6-A56B        TCGA-A6-A5ZU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6899 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965        TCGA-AD-A5EJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AD-A5EK        TCGA-AM-5820        TCGA-AM-5821        TCGA-AU-3779 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AY-A54L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AY-A69D        TCGA-AY-A71X        TCGA-AY-A8YK        TCGA-AZ-4308 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4614        TCGA-AZ-4615 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-4684        TCGA-AZ-5403 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5256        TCGA-CA-5796 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CK-4951        TCGA-CK-4952        TCGA-CK-5913        TCGA-CK-5914 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-4751        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6530        TCGA-D5-6531        TCGA-D5-6532 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A280 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A282        TCGA-DM-A288        TCGA-DM-A28A        TCGA-DM-A28C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A28K        TCGA-DM-A28M        TCGA-F4-6459        TCGA-F4-6460 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6461        TCGA-F4-6463        TCGA-F4-6569        TCGA-F4-6570 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6295 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6297        TCGA-G4-6299        TCGA-G4-6302        TCGA-G4-6303 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6311        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6320 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6322        TCGA-G4-6323        TCGA-G4-6626        TCGA-G4-6627 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-NH-A50T        TCGA-NH-A50U        TCGA-NH-A50V        TCGA-NH-A5IV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-NH-A6GA        TCGA-NH-A6GB        TCGA-NH-A6GC        TCGA-NH-A8F8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-QG-A5YV        TCGA-QG-A5YW        TCGA-QG-A5YX        TCGA-QG-A5Z1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-QG-A5Z2        TCGA-QL-A97D        TCGA-RU-A8FL        TCGA-SS-A7HO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-T9-A92H        TCGA-WS-AB45 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D44V13, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0   1
  2P LOSS WILD-TYPE   4 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    1
  2P LOSS WILD-TYPE    4  268
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               1               268
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED     6   1
  2Q LOSS WILD-TYPE 329 100
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7               429 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1               100 
$`2Q LOSS MUTATED`
TCGA-AA-3522 TCGA-AA-3560 TCGA-AA-3939 TCGA-AA-3511 TCGA-AA-3666 TCGA-AA-3842 
       37.05        19.99        12.99         6.97         2.01        37.02 
TCGA-CA-5797 
       12.59 

$`2Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 
       19.04        14.93        31.07        24.03        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       33.01         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        3.19        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       60.13        11.90        70.03 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.01              0.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            37.05            148.01 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            12.99             22.09 
[1] "2.0 - 37.0 (13.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2Q LOSS MUTATED         0        0        1         3         0         0
  2Q LOSS WILD-TYPE      74        1       28       129        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           1          1          0          1        0
  2Q LOSS WILD-TYPE        19          7         59         40       45
                   vv
clus                STAGE IVA STAGE IVB
  2Q LOSS MUTATED           0         0
  2Q LOSS WILD-TYPE        17         2
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  0                74
  STAGE IA                 0                 1
  STAGE II                 1                28
  STAGE IIA                3               129
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                19
  STAGE IIIA               1                 7
  STAGE IIIB               0                59
  STAGE IIIC               1                40
  STAGE IV                 0                45
  STAGE IVA                0                17
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     0   1   5   1
  2Q LOSS WILD-TYPE  11  76 300  54
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                11
  T2               1                76
  T3               5               300
  T4               1                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  2Q LOSS MUTATED     4   2   1
  2Q LOSS WILD-TYPE 258 103  81
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               4               258
  N1               2               103
  N2               1                81
[1] 3 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     7   0
  2Q LOSS WILD-TYPE 321  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    0
  2Q LOSS WILD-TYPE  321   64
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               7               321
  1               0                64
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1   6
  2Q LOSS WILD-TYPE 212 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    6
  2Q LOSS WILD-TYPE  212  230
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               1               212
  MALE                 6               230
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     6   0
  2Q LOSS WILD-TYPE 364   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      6    0
  2Q LOSS WILD-TYPE  364    9
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                6               364
  YES               0                 9
[1] 2 2
[1] FALSE
D45V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   0
  2Q LOSS WILD-TYPE 375  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    0
  2Q LOSS WILD-TYPE  375   62
                               clus
vv                              2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        7               375
  COLON MUCINOUS ADENOCARCINOMA               0                62
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     7   0   0   0
  2Q LOSS WILD-TYPE 316   4  25  25
D45V10, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               7               316
  R1               0                 4
  R2               0                25
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     1
  2Q LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           0     0
  2Q LOSS WILD-TYPE                        59   212
D45V12, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1               282 
       TCGA-A6-2677        TCGA-A6-2681        TCGA-A6-2682        TCGA-A6-4105 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6649        TCGA-AD-6548        TCGA-AD-6888        TCGA-AD-6895 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6964        TCGA-AZ-4313        TCGA-AZ-4681        TCGA-AZ-6601 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CK-5912        TCGA-DM-A285        TCGA-G4-6294 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6298        TCGA-G4-6310        TCGA-G4-6314        TCGA-G4-6321 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6628 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-NH-A8F7        TCGA-3L-AA1B        TCGA-4N-A93T        TCGA-4T-AA8H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-5M-AAT4        TCGA-5M-AAT6        TCGA-5M-AATE        TCGA-A6-2671 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2675        TCGA-A6-2676 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2678        TCGA-A6-2679        TCGA-A6-2680        TCGA-A6-2683 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2684        TCGA-A6-2685        TCGA-A6-2686        TCGA-A6-3807 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4107        TCGA-A6-5656 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660        TCGA-A6-5661 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665        TCGA-A6-5666 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5667        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6140 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6141        TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6650 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6651        TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6780        TCGA-A6-6781        TCGA-A6-6782        TCGA-A6-A565 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-A566        TCGA-A6-A567        TCGA-A6-A56B        TCGA-A6-A5ZU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-5900        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6899 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965        TCGA-AD-A5EJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-A5EK        TCGA-AM-5820        TCGA-AM-5821        TCGA-AU-3779 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AY-A54L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-A69D        TCGA-AY-A71X        TCGA-AY-A8YK        TCGA-AZ-4308 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4614        TCGA-AZ-4615 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-4684        TCGA-AZ-5403 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5256        TCGA-CA-5796 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-4951        TCGA-CK-4952        TCGA-CK-5913        TCGA-CK-5914 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-4751        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6530        TCGA-D5-6531        TCGA-D5-6532 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6932        TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A0XF        TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1D7        TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1DB        TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A280 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A282        TCGA-DM-A288        TCGA-DM-A28A        TCGA-DM-A28C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A28K        TCGA-DM-A28M        TCGA-F4-6459        TCGA-F4-6460 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6461        TCGA-F4-6463        TCGA-F4-6569        TCGA-F4-6570 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6295 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6297        TCGA-G4-6299        TCGA-G4-6302        TCGA-G4-6303 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6311        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6320 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6322        TCGA-G4-6323        TCGA-G4-6626        TCGA-G4-6627 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-NH-A50T        TCGA-NH-A50U        TCGA-NH-A50V        TCGA-NH-A5IV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-NH-A6GA        TCGA-NH-A6GB        TCGA-NH-A6GC        TCGA-NH-A8F8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-QG-A5YV        TCGA-QG-A5YW        TCGA-QG-A5YX        TCGA-QG-A5Z1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-QG-A5Z2        TCGA-QL-A97D        TCGA-RU-A8FL        TCGA-SS-A7HO 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-T9-A92H        TCGA-WS-AB45 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D45V13, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   1
  2Q LOSS WILD-TYPE   4 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    1
  2Q LOSS WILD-TYPE    4  268
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               1               268
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    40  12
  3P LOSS WILD-TYPE 295  89
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               52               384 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12                89 
$`3P LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       14.53         6.05        85.05        31.07        29.98        12.99 
TCGA-AA-3979 TCGA-5M-AAT4 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-6142 TCGA-A6-6651 
       24.00         1.61        34.65        32.45        25.08        21.76 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3680 TCGA-AA-3811 
        9.63         5.03        38.99         9.07        11.01        10.06 
TCGA-AA-3855 TCGA-AA-3866 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 
       32.05        17.03         2.01        21.99         7.96        13.94 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4614 
       32.02        31.00        16.44        14.50         0.20         5.65 
TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5862 
       12.10        12.59        12.20         2.01         8.02         5.03 
TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       14.04        11.08        11.01        20.19        17.75        25.48 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 
       43.27        17.85        13.41        11.38         7.50        31.96 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H 
        9.93        42.77        38.70        11.90 

$`3P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       14.93        24.03        24.00         2.01        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       35.11        16.57        37.05        37.25        37.02        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       36.53        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       22.52        24.13         8.38        25.18        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        61.84        56.25         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
       37.05        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01        50.04        47.05        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       36.03         0.99        31.07        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       34.03        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       22.42        27.42        26.47         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       12.69        12.36        12.46        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       55.92        20.42        18.25        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33        19.33        15.65        12.79        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        60.13        70.03 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              0.2               0.0 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            85.05            148.01 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            13.99             23.56 
[1] "0.2 - 85.0 (14.0)"  "0.0 - 148.0 (23.6)"
[1] "hr=" "1.5"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3P LOSS MUTATED         5        0        1        16         0         0
  3P LOSS WILD-TYPE      69        1       28       116        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           3          1          7          6        9
  3P LOSS WILD-TYPE        17          7         52         35       36
                   vv
clus                STAGE IVA STAGE IVB
  3P LOSS MUTATED           4         0
  3P LOSS WILD-TYPE        13         2
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  5                69
  STAGE IA                 0                 1
  STAGE II                 1                28
  STAGE IIA               16               116
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                3                17
  STAGE IIIA               1                 7
  STAGE IIIB               7                52
  STAGE IIIC               6                35
  STAGE IV                 9                36
  STAGE IVA                4                13
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P LOSS MUTATED     2   4  39   8
  3P LOSS WILD-TYPE   9  73 266  47
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               2                 9
  T2               4                73
  T3              39               266
  T4               8                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  3P LOSS MUTATED    24  16  13
  3P LOSS WILD-TYPE 238  89  69
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              24               238
  N1              16                89
  N2              13                69
[1] 3 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    34  13
  3P LOSS WILD-TYPE 294  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     34   13
  3P LOSS WILD-TYPE  294   51
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              34               294
  1              13                51
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    25  28
  3P LOSS WILD-TYPE 188 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     25   28
  3P LOSS WILD-TYPE  188  208
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              25               188
  MALE                28               208
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    47   0
  3P LOSS WILD-TYPE 323   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     47    0
  3P LOSS WILD-TYPE  323    9
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               47               323
  YES               0                 9
[1] 2 2
[1] FALSE
D46V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    49   4
  3P LOSS WILD-TYPE 333  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     49    4
  3P LOSS WILD-TYPE  333   58
                               clus
vv                              3P LOSS MUTATED 3P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       49               333
  COLON MUCINOUS ADENOCARCINOMA               4                58
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    40   0   4   3
  3P LOSS WILD-TYPE 283   4  21  22
D46V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              40               283
  R1               0                 4
  R2               4                21
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     2
  3P LOSS WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           8    23
  3P LOSS WILD-TYPE                        51   189
D46V12, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      8                51
  WHITE                                         23               189
[1] 4 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  32
  3P LOSS WILD-TYPE   3 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   32
  3P LOSS WILD-TYPE    3  237
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              32               237
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    27   7
  3Q LOSS WILD-TYPE 308  94
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               34               402 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7                94 
$`3Q LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3870 TCGA-AA-3939 TCGA-A6-4107 
       14.53         6.05        85.05        29.98        12.99        32.45 
TCGA-AA-3517 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 
       38.99        10.06        32.05         2.01        21.99         7.96 
TCGA-AA-A004 TCGA-AA-A01F TCGA-AD-A5EK TCGA-AY-6196 TCGA-AZ-6600 TCGA-CA-6716 
       13.94        32.02        16.44         0.20        12.10        12.20 
TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       13.02         5.03        11.08        11.01        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA 
       25.48        43.27        17.85        13.41        11.38         7.50 
TCGA-F4-6460 TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H 
       31.96        42.77        38.70        11.90 

$`3Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       14.93        31.07        24.03        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       79.69        17.85        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       37.25        37.02        34.65        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 
       16.08        13.05        34.06        25.02        27.02        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       22.42        27.42        26.47         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 
       37.02        25.02        26.04         8.02        27.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       20.42        18.25        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33         9.93        15.65        12.79        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        60.13        70.03 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              0.2               0.0 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            85.05            148.01 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           14.235            22.750 
[1] "0.2 - 85.0 (14.2)"  "0.0 - 148.0 (22.8)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3Q LOSS MUTATED         3        0        1        14         0         0
  3Q LOSS WILD-TYPE      71        1       28       118        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           1          0          4          3        5
  3Q LOSS WILD-TYPE        19          8         55         38       40
                   vv
clus                STAGE IVA STAGE IVB
  3Q LOSS MUTATED           2         0
  3Q LOSS WILD-TYPE        15         2
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  3                71
  STAGE IA                 0                 1
  STAGE II                 1                28
  STAGE IIA               14               118
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                19
  STAGE IIIA               0                 8
  STAGE IIIB               4                55
  STAGE IIIC               3                38
  STAGE IV                 5                40
  STAGE IVA                2                15
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED     0   3  26   5
  3Q LOSS WILD-TYPE  11  74 279  50
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                11
  T2               3                74
  T3              26               279
  T4               5                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  3Q LOSS MUTATED    19   8   7
  3Q LOSS WILD-TYPE 243  97  75
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              19               243
  N1               8                97
  N2               7                75
[1] 3 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    23   7
  3Q LOSS WILD-TYPE 305  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     23    7
  3Q LOSS WILD-TYPE  305   57
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              23               305
  1               7                57
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    14  20
  3Q LOSS WILD-TYPE 199 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     14   20
  3Q LOSS WILD-TYPE  199  216
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              14               199
  MALE                20               216
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    30   0
  3Q LOSS WILD-TYPE 340   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     30    0
  3Q LOSS WILD-TYPE  340    9
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               30               340
  YES               0                 9
[1] 2 2
[1] FALSE
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    31   3
  3Q LOSS WILD-TYPE 351  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     31    3
  3Q LOSS WILD-TYPE  351   59
                               clus
vv                              3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       31               351
  COLON MUCINOUS ADENOCARCINOMA               3                59
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    27   0   2   1
  3Q LOSS WILD-TYPE 296   4  23  24
D47V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              27               296
  R1               0                 4
  R2               2                23
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     1
  3Q LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           6    15
  3Q LOSS WILD-TYPE                        53   197
D47V12, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      6                53
  WHITE                                         15               197
[1] 4 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  22
  3Q LOSS WILD-TYPE   4 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   22
  3Q LOSS WILD-TYPE    4  247
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              22               247
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    97  35
  4P LOSS WILD-TYPE 238  66
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              132               304 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               35                66 
$`4P LOSS MUTATED`
TCGA-A6-2682 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       13.94        37.05        34.03        13.02        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       36.00        85.05        31.07        24.03        29.98        12.99 
TCGA-AA-3972 TCGA-AA-3976 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 
       50.99        26.01        49.08         5.88        23.51        63.62 
TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 
       91.79         4.80         1.61        39.45        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-4107 
       44.91        35.11        16.57        37.05        37.02        32.45 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 
       30.44        29.19        29.16        25.18        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3517 
       20.28        61.84         9.63         5.03         7.04        38.99 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3679 
       29.00        26.01        21.01         2.01        50.04        15.02 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       37.05        10.06        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3930 
       10.06        33.07         0.99        31.07        17.03         2.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C 
       20.98         2.01        21.99        34.03        42.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       32.02        31.00        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
        2.01        41.00         5.79        22.42        26.47        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 
        0.95        33.01         0.20        17.85         5.65         5.13 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5797 
       65.00        12.10        29.56         3.19        12.46        12.59 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
        8.02        29.06        22.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       29.03        13.02        15.02        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       10.06        45.40        56.09        20.19        17.75        25.48 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1D9 
       14.30         9.04        13.41        11.38        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6807 TCGA-F4-6808 
        7.50        44.32        14.04        26.47        43.04        33.67 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U 
       47.41         8.35        61.91        46.75        18.18        10.98 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       16.80        42.77        29.46        21.90        60.13        11.90 

$`4P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 
       13.02        24.03        36.03         8.05        19.07         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 
       17.95        23.01        19.99         0.92        19.00        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3979 TCGA-AA-3986 
       19.04        14.93        24.00         2.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 
       10.88        75.95       106.75       100.01         1.94        28.21 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 
       35.93        22.09        35.80        26.17        79.69        17.85 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 
       15.62        12.66         9.53        43.76        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       42.28        37.25        34.65        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 
       27.09        22.52        24.13         8.38        25.08        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.69        24.39        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
       56.25         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02         1.02         9.07        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 
       29.00        12.99        14.01        33.99        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       14.01        47.05        47.01        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       15.95         0.00         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       53.00        27.02        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       26.01        34.03        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        34.98        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        51.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 
       18.05        40.96        12.16        83.24        24.53        27.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 
       16.44         0.46         0.92        27.09        16.31        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        32.94        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        6.77         5.23        11.74        12.69        12.36        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02        25.02        26.04        27.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       12.00        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.01        12.95        11.08        12.03        54.61        19.59 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.42        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.39        10.13        12.43         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       92.75        49.91        13.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 
       13.25         0.53        35.31       133.18        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 
       39.42        36.00        26.43        26.04        13.78        74.79 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YX 
       19.33        19.33         9.93        15.65        12.79        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
        8.42        31.30        38.70        70.03 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              0.2               0.0 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           140.38            148.01 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           22.225            22.045 
[1] "0.2 - 140.4 (22.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4P LOSS MUTATED        16        0        6        35         3         0
  4P LOSS WILD-TYPE      58        1       23        97         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           5          5         14         15       26
  4P LOSS WILD-TYPE        15          3         45         26       19
                   vv
clus                STAGE IVA STAGE IVB
  4P LOSS MUTATED           7         1
  4P LOSS WILD-TYPE        10         1
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 16                58
  STAGE IA                 0                 1
  STAGE II                 6                23
  STAGE IIA               35                97
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                5                15
  STAGE IIIA               5                 3
  STAGE IIIB              14                45
  STAGE IIIC              15                26
  STAGE IV                26                19
  STAGE IVA                7                10
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P LOSS MUTATED     4  20  91  22
  4P LOSS WILD-TYPE   7  57 214  33
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               4                 7
  T2              20                57
  T3              91               214
  T4              22                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4P LOSS MUTATED    65  37  35
  4P LOSS WILD-TYPE 197  68  47
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              65               197
  N1              37                68
  N2              35                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"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    84  34
  4P LOSS WILD-TYPE 244  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     84   34
  4P LOSS WILD-TYPE  244   30
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              84               244
  1              34                30
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    64  73
  4P LOSS WILD-TYPE 149 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     64   73
  4P LOSS WILD-TYPE  149  163
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              64               149
  MALE                73               163
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   113   4
  4P LOSS WILD-TYPE 257   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    113    4
  4P LOSS WILD-TYPE  257    5
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              113               257
  YES               4                 5
[1] 2 2
[1] FALSE
D48V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   126  10
  4P LOSS WILD-TYPE 256  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    126   10
  4P LOSS WILD-TYPE  256   52
                               clus
vv                              4P LOSS MUTATED 4P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                      126               256
  COLON MUCINOUS ADENOCARCINOMA              10                52
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    95   1  13   5
  4P LOSS WILD-TYPE 228   3  12  20
D48V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              95               228
  R1               1                 3
  R2              13                12
  RX               5                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          21    62
  4P LOSS WILD-TYPE                        38   150
D48V12, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     21                38
  WHITE                                         62               150
[1] 4 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     3  77
  4P LOSS WILD-TYPE   1 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3   77
  4P LOSS WILD-TYPE    1  192
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              77               192
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    88  34
  4Q LOSS WILD-TYPE 247  67
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              122               314 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34                67 
$`4Q LOSS MUTATED`
TCGA-A6-2682 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       13.94        37.05        34.03        13.02        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       36.00        85.05        31.07        50.99        26.01        24.00 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6625 TCGA-4N-A93T 
       49.08         5.88        23.51        63.62        91.79         4.80 
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2683 
        1.61        39.45        43.76        43.43        35.11        16.57 
TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6651 
       37.05        32.45        30.44        29.19        29.16        21.76 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 
       23.87        20.28        61.84         9.63         5.03        38.99 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 
       29.00        26.01        33.99        21.01         2.01        50.04 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       37.05        10.06        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3955 
       10.06        33.07         0.99        17.03         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F 
        2.01        21.99        34.03        42.02        15.02        32.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W 
       33.04        26.01         2.96        39.98         2.01        41.00 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        5.79        22.42        26.47        14.50        16.31         0.95 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 
        0.20        17.85         5.13        65.00        12.10        29.56 
TCGA-CA-5256 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       12.46        14.30         8.02        13.02        29.06        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
        5.03        15.02        17.03        14.04        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 
       15.02        11.01        11.08        11.01        45.40        56.09 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6926 TCGA-D5-6929 
       20.19        17.75        25.48        43.27         9.04        13.41 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 
      140.38         7.50        44.32        14.04        26.47        31.96 
TCGA-F4-6807 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6626 TCGA-NH-A50T 
       43.04        47.41         8.35        61.91        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D 
       10.98         9.93        16.80        42.77        29.46        21.90 
TCGA-SS-A7HO TCGA-T9-A92H 
       60.13        11.90 

$`4Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 
       13.02        24.03        36.03         8.05        19.07         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 
       17.95        23.01        19.99         0.92        19.00        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
        2.01        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        28.21        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2671 
       79.69        17.85        15.62        12.66         9.53        43.76 
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2685 TCGA-A6-2686 
       46.65        42.90        42.28        44.91        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       34.65        32.75        36.53        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       24.39        20.12        19.66        16.24        24.92        56.25 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02         1.02         9.07        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       29.00        12.99        14.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       15.95         0.00         0.00         0.00        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       31.07        53.00        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       33.01        26.01        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O 
        1.02         1.02        37.02        51.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       24.53        27.42        16.44         0.46         0.92        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 
      109.28        58.39         1.41         5.65        32.94        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        49.41         6.77         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       26.04        27.02        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       12.99        14.04        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       12.03        54.61        19.59        55.92        20.42        18.25 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       13.32        12.59       131.51       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
        0.53        35.31       133.18        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V 
       36.00        26.43        26.04        13.78        74.79        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       19.33        15.65        12.79        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 
       38.70        70.03 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              0.2               0.0 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           140.38            148.01 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           22.225            22.045 
[1] "0.2 - 140.4 (22.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4Q LOSS MUTATED        14        0        5        33         2         0
  4Q LOSS WILD-TYPE      60        1       24        99         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           4          5         16         17       21
  4Q LOSS WILD-TYPE        16          3         43         24       24
                   vv
clus                STAGE IVA STAGE IVB
  4Q LOSS MUTATED           5         0
  4Q LOSS WILD-TYPE        12         2
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 14                60
  STAGE IA                 0                 1
  STAGE II                 5                24
  STAGE IIA               33                99
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                4                16
  STAGE IIIA               5                 3
  STAGE IIIB              16                43
  STAGE IIIC              17                24
  STAGE IV                21                24
  STAGE IVA                5                12
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q LOSS MUTATED     3  19  83  20
  4Q LOSS WILD-TYPE   8  58 222  35
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               3                 8
  T2              19                58
  T3              83               222
  T4              20                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4Q LOSS MUTATED    58  36  31
  4Q LOSS WILD-TYPE 204  69  51
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              58               204
  N1              36                69
  N2              31                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"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    81  26
  4Q LOSS WILD-TYPE 247  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     81   26
  4Q LOSS WILD-TYPE  247   38
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              81               247
  1              26                38
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    60  65
  4Q LOSS WILD-TYPE 153 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     60   65
  4Q LOSS WILD-TYPE  153  171
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              60               153
  MALE                65               171
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   105   4
  4Q LOSS WILD-TYPE 265   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    105    4
  4Q LOSS WILD-TYPE  265    5
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              105               265
  YES               4                 5
[1] 2 2
[1] FALSE
D49V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   113  11
  4Q LOSS WILD-TYPE 269  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    113   11
  4Q LOSS WILD-TYPE  269   51
                               clus
vv                              4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                      113               269
  COLON MUCINOUS ADENOCARCINOMA              11                51
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED    87   2  10   6
  4Q LOSS WILD-TYPE 236   2  15  19
D49V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              87               236
  R1               2                 2
  R2              10                15
  RX               6                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          22    56
  4Q LOSS WILD-TYPE                        37   156
D49V12, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     22                37
  WHITE                                         56               156
[1] 4 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     3  72
  4Q LOSS WILD-TYPE   1 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3   72
  4Q LOSS WILD-TYPE    1  197
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              72               197
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    43  16
  5P LOSS WILD-TYPE 292  85
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               59               377 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               16                85 
$`5P LOSS MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3697 TCGA-CK-5912 TCGA-5M-AAT4 
       13.94        14.53        24.16        85.05        49.08         1.61 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-3810 TCGA-A6-5660 
       39.45        43.76        43.76        42.28        36.53        29.19 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 
       32.71        27.09        25.18        23.87         9.63         5.03 
TCGA-AA-3538 TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3848 TCGA-AA-3851 
       26.01        50.04        10.06        36.95        10.06        33.07 
TCGA-AA-3854 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
       36.03        24.00         2.01        34.03        27.02        42.02 
TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 
       10.98        33.04        41.00        22.42        26.47        16.31 
TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6605 TCGA-CM-4750 
       17.26         5.65        65.00        62.79         5.23         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6164 
       13.02        29.06        22.03         5.03        15.02        29.03 
TCGA-CM-6172 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-G4-6295 
       11.01        17.85        10.13        12.43         9.04         8.35 
TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-QL-A97D 
       36.00        18.18        10.98        42.77        21.90 

$`5P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60         1.02        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01         1.94         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 
       79.69        17.85        15.62         4.80        12.66         9.53 
TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       46.65        43.43        42.90        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 
       37.05        37.25        37.02        34.65        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.06        29.16        22.52        24.13         8.38        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 
       20.28        16.24        24.92        61.84        56.25         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 
       38.99        37.02         0.00        17.03         0.00         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       30.02        18.05        18.05         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       16.44         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
       33.01         0.20        21.44        17.82        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       20.02        37.02        25.02        26.04        27.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       30.08        32.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25        25.48        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 
       12.49        16.14        15.58         7.53        12.39        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 
       55.04        85.48        39.42        61.91        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       13.78        46.75        74.79        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        16.80        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        38.70        60.13        11.90        70.03 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1.61              0.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            85.05            148.01 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            24.00             21.99 
[1] "1.6 - 85.0 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5P LOSS MUTATED         9        0        4        10         0         1
  5P LOSS WILD-TYPE      65        1       25       122        10         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           2          3         10          9        5
  5P LOSS WILD-TYPE        18          5         49         32       40
                   vv
clus                STAGE IVA STAGE IVB
  5P LOSS MUTATED           6         0
  5P LOSS WILD-TYPE        11         2
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  9                65
  STAGE IA                 0                 1
  STAGE II                 4                25
  STAGE IIA               10               122
  STAGE IIB                0                10
  STAGE IIC                1                 0
  STAGE III                2                18
  STAGE IIIA               3                 5
  STAGE IIIB              10                49
  STAGE IIIC               9                32
  STAGE IV                 5                40
  STAGE IVA                6                11
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED     1  10  39  10
  5P LOSS WILD-TYPE  10  67 266  45
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               1                10
  T2              10                67
  T3              39               266
  T4              10                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5P LOSS MUTATED    28  19  13
  5P LOSS WILD-TYPE 234  86  69
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              28               234
  N1              19                86
  N2              13                69
[1] 3 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    41  11
  5P LOSS WILD-TYPE 287  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     41   11
  5P LOSS WILD-TYPE  287   53
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              41               287
  1              11                53
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    27  33
  5P LOSS WILD-TYPE 186 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     27   33
  5P LOSS WILD-TYPE  186  203
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              27               186
  MALE                33               203
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    56   1
  5P LOSS WILD-TYPE 314   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     56    1
  5P LOSS WILD-TYPE  314    8
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               56               314
  YES               1                 8
[1] 2 2
[1] FALSE
D50V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    55   5
  5P LOSS WILD-TYPE 327  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     55    5
  5P LOSS WILD-TYPE  327   57
                               clus
vv                              5P LOSS MUTATED 5P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       55               327
  COLON MUCINOUS ADENOCARCINOMA               5                57
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    40   2   1   3
  5P LOSS WILD-TYPE 283   2  24  22
D50V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              40               283
  R1               2                 2
  R2               1                24
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                          11    32
  5P LOSS WILD-TYPE                        48   180
D50V12, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     11                48
  WHITE                                         32               180
[1] 4 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     3  37
  5P LOSS WILD-TYPE   1 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   37
  5P LOSS WILD-TYPE    1  232
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              37               232
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    55  23
  5Q LOSS WILD-TYPE 280  78
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               78               358 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23                78 
$`5Q LOSS MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3697 
       13.94        14.53        24.16        13.02        19.99        85.05 
TCGA-AA-3867 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6625 TCGA-5M-AAT4 
       24.03         1.94        49.08         5.88        91.79         1.61 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 
       39.45        43.76        43.76        37.02        36.53        30.44 
TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU 
       29.19        27.09        25.18        21.76        23.87         9.63 
TCGA-AA-3488 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3841 
        5.03        26.01        12.99        50.04        10.06        36.95 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 
       10.06        33.07        31.07        24.00         2.01        21.99 
TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02H 
       34.03        27.02        42.02        10.98        33.04         2.01 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 
       41.00        22.42        27.42        26.47        16.31         0.20 
TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6605 TCGA-CA-5797 
       17.26         5.65        65.00        62.79         5.23        12.59 
TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
       14.30         8.02        13.02        22.03         5.03        15.02 
TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       29.03        13.02        17.85        10.13        12.43         9.04 
TCGA-D5-6929 TCGA-DM-A1DB TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6297 
       13.41        44.32         8.61         1.55         8.35        82.39 
TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-QL-A97D TCGA-RU-A8FL 
       36.00        18.18        10.98        42.77        21.90        38.70 

$`5Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60         1.02        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       36.00        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-G4-6294 
       25.08        10.88        75.95       106.75       100.01        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 
       79.69        17.85        15.62         4.80        12.66         9.53 
TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       46.65        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 
       16.57        37.05        37.25        34.65        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        22.52        24.13         8.38        25.08 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        56.25         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       29.00        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
        0.00        17.03         0.00         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
        0.99        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
        2.01        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
        4.01         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96        39.98         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        5.79        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
        0.95        33.01        21.44        17.82        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       25.02        26.04        27.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       14.04        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 
       16.14        15.58         7.53        12.39        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38         7.50       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24        95.18        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
      133.18        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 
       55.04        85.48        39.42        61.91        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       13.78        46.75        74.79        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        16.80        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        60.13        11.90        70.03 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              0.2               0.0 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            91.79            148.01 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           21.945            22.090 
[1] "0.2 - 91.8 (21.9)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.6"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5Q LOSS MUTATED        11        0        4        16         0         0
  5Q LOSS WILD-TYPE      63        1       25       116        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           2          3         11         14       11
  5Q LOSS WILD-TYPE        18          5         48         27       34
                   vv
clus                STAGE IVA STAGE IVB
  5Q LOSS MUTATED           6         0
  5Q LOSS WILD-TYPE        11         2
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 11                63
  STAGE IA                 0                 1
  STAGE II                 4                25
  STAGE IIA               16               116
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                2                18
  STAGE IIIA               3                 5
  STAGE IIIB              11                48
  STAGE IIIC              14                27
  STAGE IV                11                34
  STAGE IVA                6                11
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED     1  12  57  10
  5Q LOSS WILD-TYPE  10  65 248  45
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               1                10
  T2              12                65
  T3              57               248
  T4              10                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5Q LOSS MUTATED    36  19  25
  5Q LOSS WILD-TYPE 226  86  57
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              36               226
  N1              19                86
  N2              25                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"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    50  17
  5Q LOSS WILD-TYPE 278  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     50   17
  5Q LOSS WILD-TYPE  278   47
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              50               278
  1              17                47
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    33  47
  5Q LOSS WILD-TYPE 180 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     33   47
  5Q LOSS WILD-TYPE  180  189
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              33               180
  MALE                47               189
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    70   1
  5Q LOSS WILD-TYPE 300   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     70    1
  5Q LOSS WILD-TYPE  300    8
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               70               300
  YES               1                 8
[1] 2 2
[1] FALSE
D51V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    73   7
  5Q LOSS WILD-TYPE 309  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     73    7
  5Q LOSS WILD-TYPE  309   55
                               clus
vv                              5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       73               309
  COLON MUCINOUS ADENOCARCINOMA               7                55
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    52   2   4   4
  5Q LOSS WILD-TYPE 271   2  21  21
D51V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              52               271
  R1               2                 2
  R2               4                21
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     2
  5Q LOSS WILD-TYPE                                0     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          13    40
  5Q LOSS WILD-TYPE                        46   172
D51V12, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     13                46
  WHITE                                         40               172
[1] 4 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     3  49
  5Q LOSS WILD-TYPE   1 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   49
  5Q LOSS WILD-TYPE    1  220
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              49               220
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    22  10
  6P LOSS WILD-TYPE 313  91
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               32               404 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10                91 
$`6P LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3939 TCGA-A6-2671 TCGA-A6-2678 
       24.16        36.00        19.04        12.99        43.76        42.28 
TCGA-A6-2686 TCGA-A6-6782 TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3837 TCGA-AA-3841 
       37.02        20.28        13.94         2.01        38.99        36.95 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00J TCGA-AA-A01X TCGA-AD-6899 
       18.05        24.00         2.01        18.05        26.01         5.79 
TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       16.44         5.65         3.19        12.69        12.36        12.46 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6898 
       11.08        11.01        45.40        20.19        17.75         7.53 
TCGA-DM-A1D7 TCGA-F4-6808 
       13.32        33.67 

$`6P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 
       19.99         6.05         0.92        19.00        85.05        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
      106.75       100.01         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       91.79        79.69        17.85        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        1.61         9.53        39.45        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.90        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       27.02        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 
       83.24        24.53        22.42        27.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 
       12.10        29.56         5.23        11.74        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        10.06        12.03        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.42        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       47.41        35.31       133.18         8.35        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       39.42        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       32.98         8.42        31.30        21.90        38.70        60.13 
TCGA-T9-A92H TCGA-WS-AB45 
       11.90        70.03 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             2.01              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            45.40            148.01 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            17.90             22.47 
[1] "2.0 - 45.4 (17.9)"  "0.0 - 148.0 (22.5)"
[1] "hr=" "2"  
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6P LOSS MUTATED         6        0        1        13         1         0
  6P LOSS WILD-TYPE      68        1       28       119         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           2          0          3          1        3
  6P LOSS WILD-TYPE        18          8         56         40       42
                   vv
clus                STAGE IVA STAGE IVB
  6P LOSS MUTATED           3         0
  6P LOSS WILD-TYPE        14         2
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  6                68
  STAGE IA                 0                 1
  STAGE II                 1                28
  STAGE IIA               13               119
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                2                18
  STAGE IIIA               0                 8
  STAGE IIIB               3                56
  STAGE IIIC               1                40
  STAGE IV                 3                42
  STAGE IVA                3                14
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED     2   5  19   7
  6P LOSS WILD-TYPE   9  72 286  48
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               2                 9
  T2               5                72
  T3              19               286
  T4               7                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  6P LOSS MUTATED    20   8   5
  6P LOSS WILD-TYPE 242  97  77
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              20               242
  N1               8                97
  N2               5                77
[1] 3 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    22   6
  6P LOSS WILD-TYPE 306  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     22    6
  6P LOSS WILD-TYPE  306   58
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              22               306
  1               6                58
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    13  20
  6P LOSS WILD-TYPE 200 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     13   20
  6P LOSS WILD-TYPE  200  216
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              13               200
  MALE                20               216
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    27   2
  6P LOSS WILD-TYPE 343   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     27    2
  6P LOSS WILD-TYPE  343    7
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               27               343
  YES               2                 7
[1] 2 2
[1] FALSE
D52V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    27   5
  6P LOSS WILD-TYPE 355  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     27    5
  6P LOSS WILD-TYPE  355   57
                               clus
vv                              6P LOSS MUTATED 6P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       27               355
  COLON MUCINOUS ADENOCARCINOMA               5                57
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    21   0   1   5
  6P LOSS WILD-TYPE 302   4  24  20
D52V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              21               302
  R1               0                 4
  R2               1                24
  RX               5                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     3
  6P LOSS WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           1    17
  6P LOSS WILD-TYPE                        58   195
D52V12, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      1                58
  WHITE                                         17               195
[1] 4 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     0  19
  6P LOSS WILD-TYPE   4 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   19
  6P LOSS WILD-TYPE    4  250
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              19               250
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    31  13
  6Q LOSS WILD-TYPE 304  88
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               44               392 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               13                88 
$`6Q LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3870 
       24.16        13.02        36.00        19.04        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-4107 TCGA-A6-6782 
       12.99         2.01        43.76        42.28        32.45        20.28 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3875 
       13.94        61.02         2.01        38.99        36.95        18.05 
TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00J TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02H 
       24.00         2.01        18.05        10.98        26.01         2.01 
TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        5.79        16.44         0.46         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 
       12.46        11.01        13.05        11.08        11.01        45.40 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-DM-A1D7 TCGA-F4-6704 
       20.19        17.75        15.12         7.53        13.32         1.55 
TCGA-F4-6808 TCGA-NH-A6GA 
       33.67         9.93 

$`6Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       34.03         0.99        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        6.05         0.92        19.00        85.05        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.03        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
        4.80        12.66         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.43        42.90        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3663 
       21.01        24.00        29.95        20.98        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       17.03        27.02        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96        39.98         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 
       24.53        22.42        27.42        26.47         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       29.56         5.23        11.74        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       15.02        14.04        12.95        11.08        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
        6.18        47.87        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       32.98         8.42        31.30        21.90        38.70        60.13 
TCGA-T9-A92H TCGA-WS-AB45 
       11.90        70.03 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.46              0.00 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            61.02            148.01 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            14.53             23.03 
[1] "0.5 - 61.0 (14.5)"  "0.0 - 148.0 (23.0)"
[1] "hr=" "2"  
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6Q LOSS MUTATED         6        0        2        12         1         0
  6Q LOSS WILD-TYPE      68        1       27       120         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           2          0          7          6        5
  6Q LOSS WILD-TYPE        18          8         52         35       40
                   vv
clus                STAGE IVA STAGE IVB
  6Q LOSS MUTATED           3         1
  6Q LOSS WILD-TYPE        14         1
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  6                68
  STAGE IA                 0                 1
  STAGE II                 2                27
  STAGE IIA               12               120
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                2                18
  STAGE IIIA               0                 8
  STAGE IIIB               7                52
  STAGE IIIC               6                35
  STAGE IV                 5                40
  STAGE IVA                3                14
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED     2   5  30   8
  6Q LOSS WILD-TYPE   9  72 275  47
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               2                 9
  T2               5                72
  T3              30               275
  T4               8                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  6Q LOSS MUTATED    20  11  14
  6Q LOSS WILD-TYPE 242  94  68
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              20               242
  N1              11                94
  N2              14                68
[1] 3 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    28   9
  6Q LOSS WILD-TYPE 300  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     28    9
  6Q LOSS WILD-TYPE  300   55
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              28               300
  1               9                55
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    19  26
  6Q LOSS WILD-TYPE 194 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     19   26
  6Q LOSS WILD-TYPE  194  210
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              19               194
  MALE                26               210
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    34   2
  6Q LOSS WILD-TYPE 336   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     34    2
  6Q LOSS WILD-TYPE  336    7
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               34               336
  YES               2                 7
[1] 2 2
[1] FALSE
D53V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    37   7
  6Q LOSS WILD-TYPE 345  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     37    7
  6Q LOSS WILD-TYPE  345   55
                               clus
vv                              6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       37               345
  COLON MUCINOUS ADENOCARCINOMA               7                55
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    31   0   2   6
  6Q LOSS WILD-TYPE 292   4  23  19
D53V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              31               292
  R1               0                 4
  R2               2                23
  RX               6                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  1     3
  6Q LOSS WILD-TYPE                                0     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    19
  6Q LOSS WILD-TYPE                        56   193
D53V12, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      3                56
  WHITE                                         19               193
[1] 4 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     0  24
  6Q LOSS WILD-TYPE   4 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   24
  6Q LOSS WILD-TYPE    4  245
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              24               245
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     4   0
  7Q LOSS WILD-TYPE 331 101
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               432 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0               101 
$`7Q LOSS MUTATED`
TCGA-5M-AATE TCGA-AU-3779 TCGA-CM-5341 TCGA-D5-6932 
       39.45        14.50        29.06        11.38 

$`7Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       17.85        15.62         4.80        12.66         1.61         9.53 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       33.04         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.92        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.36        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       26.04         8.02        27.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        38.70        60.13        11.90        70.03 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            11.38              0.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            39.45            148.01 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           21.780            22.045 
[1] "11.4 - 39.5 (21.8)" "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7Q LOSS MUTATED         0        0        0         3         0         0
  7Q LOSS WILD-TYPE      74        1       29       129        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           0          1          0          0        0
  7Q LOSS WILD-TYPE        20          7         59         41       45
                   vv
clus                STAGE IVA STAGE IVB
  7Q LOSS MUTATED           0         0
  7Q LOSS WILD-TYPE        17         2
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                74
  STAGE IA                 0                 1
  STAGE II                 0                29
  STAGE IIA                3               129
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                20
  STAGE IIIA               1                 7
  STAGE IIIB               0                59
  STAGE IIIC               0                41
  STAGE IV                 0                45
  STAGE IVA                0                17
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED     0   1   3   0
  7Q LOSS WILD-TYPE  11  76 302  55
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0                11
  T2               1                76
  T3               3               302
  T4               0                55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  7Q LOSS MUTATED     3   1   0
  7Q LOSS WILD-TYPE 259 104  82
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               3               259
  N1               1               104
  N2               0                82
[1] 3 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
  7Q LOSS MUTATED     4   0
  7Q LOSS WILD-TYPE 324  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    0
  7Q LOSS WILD-TYPE  324   64
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               4               324
  1               0                64
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2   2
  7Q LOSS WILD-TYPE 211 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    2
  7Q LOSS WILD-TYPE  211  234
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               2               211
  MALE                 2               234
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     4   0
  7Q LOSS WILD-TYPE 366   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    0
  7Q LOSS WILD-TYPE  366    9
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                4               366
  YES               0                 9
[1] 2 2
[1] FALSE
D54V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     4   0
  7Q LOSS WILD-TYPE 378  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    0
  7Q LOSS WILD-TYPE  378   62
                               clus
vv                              7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        4               378
  COLON MUCINOUS ADENOCARCINOMA               0                62
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED     4   0   0   0
  7Q LOSS WILD-TYPE 319   4  25  25
D54V10, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               4               319
  R1               0                 4
  R2               0                25
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           1     3
  7Q LOSS WILD-TYPE                        58   209
D54V12, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                58
  WHITE                                          3               209
[1] 4 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
  7Q LOSS MUTATED     1   3
  7Q LOSS WILD-TYPE   3 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    3
  7Q LOSS WILD-TYPE    3  266
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               3               266
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   101  34
  8P LOSS WILD-TYPE 234  67
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              135               301 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               34                67 
$`8P LOSS MUTATED`
TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       45.60         1.02        24.03        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 
       19.99        19.99        19.00        85.05        31.07        24.03 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6298 
       26.01        24.00       106.75         1.94         5.88        23.51 
TCGA-G4-6314 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 
       35.93        91.79         4.80         1.61         9.53        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.43        42.28        44.91        35.11        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6137 
       34.65        36.53        32.91        30.44        23.61        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        25.18        20.61        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3495 TCGA-AA-3517 
       20.28        61.84        56.25         5.03        37.05        38.99 
TCGA-AA-3529 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3660 TCGA-AA-3666 
        0.00        33.99        21.01        24.00        78.08         2.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3842 
       47.01        15.02        11.01         5.98        37.05        37.02 
TCGA-AA-3851 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3971 
       33.07        17.03        27.02         2.01        24.00        16.08 
TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A017 
       34.06        27.02         7.96        19.00        34.03        15.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6901 
       12.00        31.00         1.02        33.04        41.00        22.42 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 
       26.47        16.31        33.01         0.20        17.85       109.28 
TCGA-AZ-4614 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5797 
        5.65        62.79        12.10        29.56        11.74        12.59 
TCGA-CA-6719 TCGA-CK-4952 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       14.30        15.62        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
       32.02         5.03        14.04        21.99        13.02        15.02 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6534 
       13.05        11.08        10.06        54.61        56.09        43.27 
TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       15.12        12.49        10.13         9.04        13.41        11.38 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28A 
      130.65        49.91        13.32       140.38       131.51        26.47 
TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6854 TCGA-G4-6299 
       60.79        31.96        35.74         1.55         0.53        74.56 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       61.91        36.00        26.43        10.98        19.33         9.93 
TCGA-NH-A8F8 TCGA-QL-A97D TCGA-RU-A8FL 
       16.80        21.90        38.70 

$`8P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        14.53        24.16        58.03        13.02 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3554 
       37.05        36.03         8.05        19.07         0.99        17.95 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        6.05         0.92        36.00        19.04        19.04        14.93 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3986 
       29.98        12.99        24.00         2.01        50.99        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6310 
       10.88        75.95       100.01        49.08        28.21        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       22.09        35.80        26.17        79.69        17.85        15.62 
TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 
       12.66        39.45        46.65        42.90        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       37.02        32.75        32.45        31.63        29.19        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        29.16        22.52         8.38 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       21.76        24.39        20.12        19.66        16.24        24.92 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
        9.63         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 
        6.97         1.02         1.02         9.07        19.07        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3555 TCGA-AA-3558 
       29.00        26.01        12.99        14.01        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02         6.97        54.02        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       47.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 
       32.05         0.99        31.07        53.00        18.05        31.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       13.05        25.02        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        35.01         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       83.24        24.53         5.79        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.92        14.50        27.09         0.95        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       17.26        19.33        18.84        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        22.36        65.00        88.21        49.41         6.77 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        70.16        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 
       26.04         8.02        27.02        29.06        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       14.99        12.99        14.04        11.01        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       11.01        12.03        45.40        19.59        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 
       20.42        17.75        18.25        25.48        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       17.13        16.14        15.58         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA 
      119.70        24.43        38.20        92.75        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C 
       44.32       135.65         7.76       139.17        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
      119.93        35.97       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       11.11        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        33.67        13.25        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        8.35        82.39        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       55.04        85.48        39.42        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV 
       74.79        18.18        19.33        15.65        12.79        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H 
       29.46        32.98         8.42        31.30        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                 0 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           140.38            148.01 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            24.00             21.37 
[1] "0.0 - 140.4 (24.0)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8P LOSS MUTATED        15        0        7        31         2         0
  8P LOSS WILD-TYPE      59        1       22       101         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           7          4         17         18       22
  8P LOSS WILD-TYPE        13          4         42         23       23
                   vv
clus                STAGE IVA STAGE IVB
  8P LOSS MUTATED           9         1
  8P LOSS WILD-TYPE         8         1
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 15                59
  STAGE IA                 0                 1
  STAGE II                 7                22
  STAGE IIA               31               101
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                7                13
  STAGE IIIA               4                 4
  STAGE IIIB              17                42
  STAGE IIIC              18                23
  STAGE IV                22                23
  STAGE IVA                9                 8
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P LOSS MUTATED     1  19  98  18
  8P LOSS WILD-TYPE  10  58 207  37
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               1                10
  T2              19                58
  T3              98               207
  T4              18                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  8P LOSS MUTATED    62  37  37
  8P LOSS WILD-TYPE 200  68  45
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              62               200
  N1              37                68
  N2              37                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"
D55V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    89  32
  8P LOSS WILD-TYPE 239  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     89   32
  8P LOSS WILD-TYPE  239   32
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              89               239
  1              32                32
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    57  79
  8P LOSS WILD-TYPE 156 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     57   79
  8P LOSS WILD-TYPE  156  157
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              57               156
  MALE                79               157
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   117   2
  8P LOSS WILD-TYPE 253   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    117    2
  8P LOSS WILD-TYPE  253    7
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              117               253
  YES               2                 7
[1] 2 2
[1] FALSE
D55V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   123  11
  8P LOSS WILD-TYPE 259  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    123   11
  8P LOSS WILD-TYPE  259   51
                               clus
vv                              8P LOSS MUTATED 8P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                      123               259
  COLON MUCINOUS ADENOCARCINOMA              11                51
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED    94   2  10   3
  8P LOSS WILD-TYPE 229   2  15  22
D55V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              94               229
  R1               2                 2
  R2              10                15
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1     2
  8P LOSS WILD-TYPE                                0     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          22    65
  8P LOSS WILD-TYPE                        37   147
D55V12, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     22                37
  WHITE                                         65               147
[1] 4 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
  8P LOSS MUTATED     3  84
  8P LOSS WILD-TYPE   1 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3   84
  8P LOSS WILD-TYPE    1  185
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 1
  NOT HISPANIC OR LATINO              84               185
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    18   7
  8Q LOSS WILD-TYPE 317  94
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               411 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7                94 
$`8Q LOSS MUTATED`
TCGA-AA-3531 TCGA-AZ-6608 TCGA-G4-6314 TCGA-G4-6625 TCGA-A6-2671 TCGA-A6-2674 
       34.03         1.94        35.93        91.79        43.76        43.76 
TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-6782 TCGA-AA-3517 TCGA-AA-3851 
       44.91        16.57        34.65        20.28        38.99        33.07 
TCGA-AA-3941 TCGA-AA-3989 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-6196 TCGA-AY-A69D 
       24.00         7.96        22.42        26.47         0.20        17.85 
TCGA-AZ-5403 TCGA-CM-5860 TCGA-CM-6679 TCGA-D5-6539 TCGA-DM-A1D6 TCGA-F4-6704 
       62.79        32.02        10.06        12.49        49.91         1.55 
TCGA-QL-A97D 
       21.90 

$`8Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 
       25.08        10.88        75.95       106.75       100.01        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       26.17        79.69        17.85        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        1.61         9.53        39.45        46.65        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       42.28        35.11        37.05        37.25        37.02        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       37.02         0.00        17.03        10.06         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        25.02        27.02        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13        22.36        65.00        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        31.30        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       60.13        11.90        70.03 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              0.2               0.0 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            91.79            148.01 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            26.47             21.99 
[1] "0.2 - 91.8 (26.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8Q LOSS MUTATED         1        0        1         8         2         0
  8Q LOSS WILD-TYPE      73        1       28       124         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0          1          0          4        5
  8Q LOSS WILD-TYPE        20          7         59         37       40
                   vv
clus                STAGE IVA STAGE IVB
  8Q LOSS MUTATED           1         0
  8Q LOSS WILD-TYPE        16         2
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  1                73
  STAGE IA                 0                 1
  STAGE II                 1                28
  STAGE IIA                8               124
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                20
  STAGE IIIA               1                 7
  STAGE IIIB               0                59
  STAGE IIIC               4                37
  STAGE IV                 5                40
  STAGE IVA                1                16
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED     0   2  19   4
  8Q LOSS WILD-TYPE  11  75 286  51
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               0                11
  T2               2                75
  T3              19               286
  T4               4                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  8Q LOSS MUTATED    15   2   8
  8Q LOSS WILD-TYPE 247 103  74
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              15               247
  N1               2               103
  N2               8                74
[1] 3 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
  8Q LOSS MUTATED    12   6
  8Q LOSS WILD-TYPE 316  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     12    6
  8Q LOSS WILD-TYPE  316   58
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              12               316
  1               6                58
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    11  14
  8Q LOSS WILD-TYPE 202 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     11   14
  8Q LOSS WILD-TYPE  202  222
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              11               202
  MALE                14               222
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    22   0
  8Q LOSS WILD-TYPE 348   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     22    0
  8Q LOSS WILD-TYPE  348    9
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               22               348
  YES               0                 9
[1] 2 2
[1] FALSE
D56V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    21   4
  8Q LOSS WILD-TYPE 361  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     21    4
  8Q LOSS WILD-TYPE  361   58
                               clus
vv                              8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       21               361
  COLON MUCINOUS ADENOCARCINOMA               4                58
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    17   1   1   0
  8Q LOSS WILD-TYPE 306   3  24  25
D56V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              17               306
  R1               1                 3
  R2               1                24
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  1     0
  8Q LOSS WILD-TYPE                                0    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           2    17
  8Q LOSS WILD-TYPE                        57   195
D56V12, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                57
  WHITE                                         17               195
[1] 4 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
  8Q LOSS MUTATED     0  18
  8Q LOSS WILD-TYPE   4 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   18
  8Q LOSS WILD-TYPE    4  251
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              18               251
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    39  11
  9P LOSS WILD-TYPE 296  90
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               50               386 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11                90 
$`9P LOSS MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 
       14.53        24.16        19.99        85.05        24.03        12.99 
TCGA-AA-3972 TCGA-AD-6888 TCGA-AZ-6608 TCGA-5M-AATE TCGA-A6-2675 TCGA-A6-3810 
       50.99        15.52         1.94        39.45        43.43        36.53 
TCGA-A6-5667 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3553 
       29.16        21.76        61.84         6.97        38.99        24.00 
TCGA-AA-3685 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-A004 TCGA-AA-A01F TCGA-AA-A01K 
       37.05        24.00        20.98        13.94        32.02        31.00 
TCGA-AA-A03J TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-6605 
       40.96        26.47        14.50        16.31         5.65         5.23 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-6169 TCGA-CM-6170 
        3.19        12.59        12.20         8.02        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       11.08        11.01        10.06        20.19        25.48        43.27 
TCGA-D5-6898 TCGA-DM-A0XF TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-NH-A6GA 
        7.53        38.20        33.67         8.35        82.39         9.93 
TCGA-NH-A8F8 TCGA-T9-A92H 
       16.80        11.90 

$`9P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        45.60        13.94         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 
        0.99        13.02        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 
       31.07        29.98        24.00         2.01        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       19.07        38.04        21.99        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 
       10.88        75.95       106.75       100.01        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       12.66         1.61         9.53        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        34.65        32.75        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        20.61        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        24.92        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       35.01        63.98         1.02         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 
       18.05        31.00         2.01        33.01        26.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       41.00        39.98        18.05        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        5.79        22.42        27.42        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10        29.56        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       12.69        12.36        12.46        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.42        17.75        18.25        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31       133.18        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV 
       10.98        19.33        19.33        15.65        12.79        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        38.70 
TCGA-SS-A7HO TCGA-WS-AB45 
       60.13        70.03 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.94              0.00 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            85.05            148.01 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           20.090            22.225 
[1] "1.9 - 85.0 (20.1)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9P LOSS MUTATED         7        0        4        15         0         0
  9P LOSS WILD-TYPE      67        1       25       117        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           1          2          7          6        7
  9P LOSS WILD-TYPE        19          6         52         35       38
                   vv
clus                STAGE IVA STAGE IVB
  9P LOSS MUTATED           3         0
  9P LOSS WILD-TYPE        14         2
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  7                67
  STAGE IA                 0                 1
  STAGE II                 4                25
  STAGE IIA               15               117
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                19
  STAGE IIIA               2                 6
  STAGE IIIB               7                52
  STAGE IIIC               6                35
  STAGE IV                 7                38
  STAGE IVA                3                14
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P LOSS MUTATED     2   8  32  11
  9P LOSS WILD-TYPE   9  69 273  44
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               2                 9
  T2               8                69
  T3              32               273
  T4              11                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  9P LOSS MUTATED    27  13  13
  9P LOSS WILD-TYPE 235  92  69
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              27               235
  N1              13                92
  N2              13                69
[1] 3 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
  9P LOSS MUTATED    38  10
  9P LOSS WILD-TYPE 290  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     38   10
  9P LOSS WILD-TYPE  290   54
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              38               290
  1              10                54
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    20  33
  9P LOSS WILD-TYPE 193 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     20   33
  9P LOSS WILD-TYPE  193  203
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              20               193
  MALE                33               203
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    49   0
  9P LOSS WILD-TYPE 321   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     49    0
  9P LOSS WILD-TYPE  321    9
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               49               321
  YES               0                 9
[1] 2 2
[1] FALSE
D57V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    51   1
  9P LOSS WILD-TYPE 331  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     51    1
  9P LOSS WILD-TYPE  331   61
                               clus
vv                              9P LOSS MUTATED 9P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       51               331
  COLON MUCINOUS ADENOCARCINOMA               1                61
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    37   2   3   2
  9P LOSS WILD-TYPE 286   2  22  23
D57V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              37               286
  R1               2                 2
  R2               3                22
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     2
  9P LOSS WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           7    27
  9P LOSS WILD-TYPE                        52   185
D57V12, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      7                52
  WHITE                                         27               185
[1] 4 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
  9P LOSS MUTATED     1  34
  9P LOSS WILD-TYPE   3 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   34
  9P LOSS WILD-TYPE    3  235
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              34               235
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    38  12
  9Q LOSS WILD-TYPE 297  89
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50               386 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               12                89 
$`9Q LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 
       24.16        19.99        85.05        24.03        12.99        50.99 
TCGA-AZ-6608 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-5667 
        1.94        39.45        43.76        43.43        36.53        29.16 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3553 
       25.08        21.76        61.84         6.97        38.99        24.00 
TCGA-AA-3685 TCGA-AA-3955 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A03J TCGA-AU-3779 
       37.05        20.98        32.02        31.00        40.96        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4614 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       16.31         0.95         5.65        29.56         5.23         3.19 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       12.59        12.20         8.02        13.02        15.02        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6898 TCGA-DM-A0XF 
       11.01        10.06        20.19        25.48         7.53        38.20 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-NH-A6GA TCGA-NH-A8F8 
       33.67         8.35        82.39        65.85         9.93        16.80 
TCGA-SS-A7HO TCGA-T9-A92H 
       60.13        11.90 

$`9Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 
       14.93        31.07        29.98        24.00         2.01        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 
       15.62         4.80        12.66         1.61         9.53        43.76 
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       46.65        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 
       37.05        37.25        37.02        34.65        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        20.61        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        24.92        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       35.01        63.98         1.02         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 
       16.44         0.46         0.92        27.09        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
      109.28        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       13.05        11.08        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       56.09        55.92        20.42        17.75        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 
        0.53        47.41        35.31       133.18        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        10.98        19.33        19.33        15.65        12.79 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-WS-AB45 
       38.70        70.03 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.95              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            85.05            148.01 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           21.370            22.075 
[1] "0.9 - 85.0 (21.4)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9Q LOSS MUTATED         8        0        4        12         1         0
  9Q LOSS WILD-TYPE      66        1       25       120         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           1          2          6          5        9
  9Q LOSS WILD-TYPE        19          6         53         36       36
                   vv
clus                STAGE IVA STAGE IVB
  9Q LOSS MUTATED           3         0
  9Q LOSS WILD-TYPE        14         2
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  8                66
  STAGE IA                 0                 1
  STAGE II                 4                25
  STAGE IIA               12               120
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                19
  STAGE IIIA               2                 6
  STAGE IIIB               6                53
  STAGE IIIC               5                36
  STAGE IV                 9                36
  STAGE IVA                3                14
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED     3   9  31  10
  9Q LOSS WILD-TYPE   8  68 274  45
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               3                 8
  T2               9                68
  T3              31               274
  T4              10                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  9Q LOSS MUTATED    26  14  13
  9Q LOSS WILD-TYPE 236  91  69
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              26               236
  N1              14                91
  N2              13                69
[1] 3 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
  9Q LOSS MUTATED    34  12
  9Q LOSS WILD-TYPE 294  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     34   12
  9Q LOSS WILD-TYPE  294   52
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              34               294
  1              12                52
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    23  30
  9Q LOSS WILD-TYPE 190 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     23   30
  9Q LOSS WILD-TYPE  190  206
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              23               190
  MALE                30               206
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    49   0
  9Q LOSS WILD-TYPE 321   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     49    0
  9Q LOSS WILD-TYPE  321    9
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               49               321
  YES               0                 9
[1] 2 2
[1] FALSE
D58V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    50   1
  9Q LOSS WILD-TYPE 332  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     50    1
  9Q LOSS WILD-TYPE  332   61
                               clus
vv                              9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       50               332
  COLON MUCINOUS ADENOCARCINOMA               1                61
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    37   1   3   2
  9Q LOSS WILD-TYPE 286   3  22  23
D58V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              37               286
  R1               1                 3
  R2               3                22
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     2
  9Q LOSS WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           8    28
  9Q LOSS WILD-TYPE                        51   184
D58V12, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      8                51
  WHITE                                         28               184
[1] 4 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
  9Q LOSS MUTATED     1  36
  9Q LOSS WILD-TYPE   3 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   36
  9Q LOSS WILD-TYPE    3  233
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              36               233
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    52  14
  10P LOSS WILD-TYPE 283  87
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                66                370 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                14                 87 
$`10P LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3692 TCGA-AA-3697 
       24.33        45.60        13.02        19.99        36.00        85.05 
TCGA-AA-3867 TCGA-AA-3972 TCGA-NH-A8F7 TCGA-A6-2680 TCGA-A6-5659 TCGA-A6-5666 
       24.03        50.99        17.85        35.11        30.44        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3494 
       29.16        22.52        25.18        23.87         9.63         1.02 
TCGA-AA-3511 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 
        6.97        50.04        37.05        10.06        31.07        17.03 
TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02W 
        7.96        34.03        42.02        10.98        26.01        41.00 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4616 
       22.42        16.44        14.50         0.20         5.65         5.13 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 
       65.00        62.79        29.56         3.19        12.59        12.20 
TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-5864 
       14.30         8.02        29.06        22.03        15.02        15.02 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6531 
       29.03        13.02        15.02        11.08        11.08        17.75 
TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 
        7.53         9.04        13.41        82.39        65.85        55.04 
TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A6GC TCGA-RU-A8FL TCGA-SS-A7HO 
       61.91        26.04        46.75        12.79        38.70        60.13 

$`10P LOSS WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 
        0.99        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       19.00        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00         2.01        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-3L-AA1B TCGA-4N-A93T 
       35.80        26.17        91.79        79.69        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 
       43.76        43.43        42.90        42.28        44.91        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        24.13         8.38        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 
       20.28        16.24        24.92        61.84        56.25         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        7.04         3.02        37.05        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01         5.98         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        36.95        37.02         0.00        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
       33.07         0.00        36.03        32.05         0.99        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02        27.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       24.53         5.79        27.42        26.47         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41        32.94        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       12.10         5.23        11.74        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.39        12.59        12.76        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
       25.02        26.04        27.02        13.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02        15.02         5.03        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       14.04        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43        14.30         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       35.31       133.18         8.35        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 
       44.68        85.48        39.42        36.00        26.43        13.78 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        11.90        70.03 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               0.2                0.0 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             85.05             148.01 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             22.47              22.01 
[1] "0.2 - 85.0 (22.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10P LOSS MUTATED        10        0        6        11         1         1
  10P LOSS WILD-TYPE      64        1       23       121         9         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           1          2         10          7       12
  10P LOSS WILD-TYPE        19          6         49         34       33
                    vv
clus                 STAGE IVA STAGE IVB
  10P LOSS MUTATED           3         1
  10P LOSS WILD-TYPE        14         1
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  10                 64
  STAGE IA                  0                  1
  STAGE II                  6                 23
  STAGE IIA                11                121
  STAGE IIB                 1                  9
  STAGE IIC                 1                  0
  STAGE III                 1                 19
  STAGE IIIA                2                  6
  STAGE IIIB               10                 49
  STAGE IIIC                7                 34
  STAGE IV                 12                 33
  STAGE IVA                 3                 14
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P LOSS MUTATED     1  13  45   8
  10P LOSS WILD-TYPE  10  64 260  47
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                1                 10
  T2               13                 64
  T3               45                260
  T4                8                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  10P LOSS MUTATED    32  19  16
  10P LOSS WILD-TYPE 230  86  66
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               32                230
  N1               19                 86
  N2               16                 66
[1] 3 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
  10P LOSS MUTATED    42  16
  10P LOSS WILD-TYPE 286  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     42   16
  10P LOSS WILD-TYPE  286   48
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               42                286
  1               16                 48
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    33  34
  10P LOSS WILD-TYPE 180 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     33   34
  10P LOSS WILD-TYPE  180  202
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               33                180
  MALE                 34                202
[1] 2 2
[1] FALSE
D59V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    61   3
  10P LOSS WILD-TYPE 309   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     61    3
  10P LOSS WILD-TYPE  309    6
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                61                309
  YES                3                  6
[1] 2 2
[1] FALSE
D59V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    61   6
  10P LOSS WILD-TYPE 321  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     61    6
  10P LOSS WILD-TYPE  321   56
                               clus
vv                              10P LOSS MUTATED 10P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        61                321
  COLON MUCINOUS ADENOCARCINOMA                6                 56
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    47   0   6   4
  10P LOSS WILD-TYPE 276   4  19  21
D59V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               47                276
  R1                0                  4
  R2                6                 19
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     3
  10P LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           8    36
  10P LOSS WILD-TYPE                        51   176
D59V12, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       8                 51
  WHITE                                          36                176
[1] 4 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
  10P LOSS MUTATED     1  45
  10P LOSS WILD-TYPE   3 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   45
  10P LOSS WILD-TYPE    3  224
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               45                224
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    57  13
  10Q LOSS WILD-TYPE 278  88
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                70                366 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                13                 88 
$`10Q LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 
       24.33        45.60        13.02        19.99         6.05        36.00 
TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3972 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-A6-2671 
       85.05        24.03        50.99        91.79        17.85        43.76 
TCGA-A6-2680 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 
       35.11        30.44        32.71        29.16        22.52        25.18 
TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3548 TCGA-AA-3673 
       23.87         9.63         1.02         6.97        33.99        50.04 
TCGA-AA-3685 TCGA-AA-3841 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-A00F 
       37.05        36.95        10.06        31.07        17.03        34.03 
TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-A5EK 
       42.02        10.98        26.01        41.00        22.42        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
       14.50        16.31         5.65        65.00        62.79        29.56 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 
        3.19        12.59        12.20        14.30         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 
       22.03         5.03        15.02        15.02        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6534 
       15.02        11.08        11.08        10.06        17.75        43.27 
TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 
        7.53         9.04        13.41        33.67        55.04        61.91 
TCGA-G4-6322 TCGA-NH-A6GC TCGA-RU-A8FL TCGA-SS-A7HO 
       26.04        12.79        38.70        60.13 

$`10Q LOSS WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 
        0.99        17.95        23.01        19.99         0.92        19.00 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        31.07        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       24.00         2.01        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       26.17        79.69        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        9.53        39.45        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       42.28        44.91        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       61.84        56.25         5.03         7.04         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
        1.02        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        27.42        26.47 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46         0.92        27.09         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
      109.28        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       12.69        12.36        12.46        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 
       13.02        22.98        30.08        32.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        14.04        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 
       12.99        14.04        11.01        12.95        13.05        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.19        20.42        18.25        25.48        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43        14.30         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 
       53.62        44.68        85.48        39.42        36.00        26.43 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        11.90        70.03 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1.02               0.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             91.79             148.01 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            23.195             21.990 
[1] "1.0 - 91.8 (23.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10Q LOSS MUTATED        11        0        6        14         1         1
  10Q LOSS WILD-TYPE      63        1       23       118         9         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           1          2         10          8       11
  10Q LOSS WILD-TYPE        19          6         49         33       34
                    vv
clus                 STAGE IVA STAGE IVB
  10Q LOSS MUTATED           4         1
  10Q LOSS WILD-TYPE        13         1
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  11                 63
  STAGE IA                  0                  1
  STAGE II                  6                 23
  STAGE IIA                14                118
  STAGE IIB                 1                  9
  STAGE IIC                 1                  0
  STAGE III                 1                 19
  STAGE IIIA                2                  6
  STAGE IIIB               10                 49
  STAGE IIIC                8                 33
  STAGE IV                 11                 34
  STAGE IVA                 4                 13
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED     2  13  47  10
  10Q LOSS WILD-TYPE   9  64 258  45
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                2                  9
  T2               13                 64
  T3               47                258
  T4               10                 45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  10Q LOSS MUTATED    36  19  17
  10Q LOSS WILD-TYPE 226  86  65
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               36                226
  N1               19                 86
  N2               17                 65
[1] 3 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
  10Q LOSS MUTATED    48  16
  10Q LOSS WILD-TYPE 280  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     48   16
  10Q LOSS WILD-TYPE  280   48
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               48                280
  1               16                 48
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    36  36
  10Q LOSS WILD-TYPE 177 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     36   36
  10Q LOSS WILD-TYPE  177  200
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               36                177
  MALE                 36                200
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    66   3
  10Q LOSS WILD-TYPE 304   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     66    3
  10Q LOSS WILD-TYPE  304    6
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                66                304
  YES                3                  6
[1] 2 2
[1] FALSE
D60V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    66   6
  10Q LOSS WILD-TYPE 316  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     66    6
  10Q LOSS WILD-TYPE  316   56
                               clus
vv                              10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        66                316
  COLON MUCINOUS ADENOCARCINOMA                6                 56
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    51   1   7   4
  10Q LOSS WILD-TYPE 272   3  18  21
D60V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               51                272
  R1                1                  3
  R2                7                 18
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     3
  10Q LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           9    37
  10Q LOSS WILD-TYPE                        50   175
D60V12, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       9                 50
  WHITE                                          37                175
[1] 4 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
  10Q LOSS MUTATED     1  47
  10Q LOSS WILD-TYPE   3 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   47
  10Q LOSS WILD-TYPE    3  222
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               47                222
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    38  10
  11P LOSS WILD-TYPE 297  91
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                48                388 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                10                 91 
$`11P LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3952 
       24.16         6.05        36.00        31.07        12.99         2.01 
TCGA-AA-3972 TCGA-CK-5912 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6138 
       50.99        49.08        36.53        32.45        30.44        22.52 
TCGA-A6-6651 TCGA-AA-3519 TCGA-AA-3666 TCGA-AA-3685 TCGA-AA-3855 TCGA-AA-3941 
       21.76         9.07         2.01        37.05        32.05        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
        2.01        21.99        42.02        32.02        31.00        33.04 
TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 
        2.96        40.96         5.79        16.44        14.50         0.20 
TCGA-AY-A69D TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CM-5862 TCGA-CM-5863 
       17.85         1.41        12.46        12.20         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6534 
       15.02        14.04        11.01        45.40        20.19        43.27 
TCGA-D5-6924 TCGA-DM-A1DA TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A6GC 
       14.30         7.50        61.91        36.00        18.18        12.79 

$`11P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 
       14.93        24.03        29.98        24.00        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.75        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       22.09        22.06        32.71        29.16        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         1.02        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       17.03        27.02        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        20.98        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       35.01         1.02         1.02        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 
       39.98        18.05        12.16        83.24        24.53        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
       27.42        26.47         0.46         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        33.01        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.39        12.59        12.59        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       32.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        54.61        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        25.48        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       47.41        35.31       133.18         8.35        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       39.42        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        15.65        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       38.70        60.13        11.90        70.03 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               0.2                0.0 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             61.91             148.01 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            19.185             22.225 
[1] "0.2 - 61.9 (19.2)"  "0.0 - 148.0 (22.2)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11P LOSS MUTATED         9        0        1        12         0         0
  11P LOSS WILD-TYPE      65        1       28       120        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           4          0          7          6        7
  11P LOSS WILD-TYPE        16          8         52         35       38
                    vv
clus                 STAGE IVA STAGE IVB
  11P LOSS MUTATED           3         1
  11P LOSS WILD-TYPE        14         1
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   9                 65
  STAGE IA                  0                  1
  STAGE II                  1                 28
  STAGE IIA                12                120
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 4                 16
  STAGE IIIA                0                  8
  STAGE IIIB                7                 52
  STAGE IIIC                6                 35
  STAGE IV                  7                 38
  STAGE IVA                 3                 14
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED     1   8  33   8
  11P LOSS WILD-TYPE  10  69 272  47
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                 10
  T2                8                 69
  T3               33                272
  T4                8                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  11P LOSS MUTATED    21  17  12
  11P LOSS WILD-TYPE 241  88  70
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               21                241
  N1               17                 88
  N2               12                 70
[1] 3 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
  11P LOSS MUTATED    31  11
  11P LOSS WILD-TYPE 297  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     31   11
  11P LOSS WILD-TYPE  297   53
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               31                297
  1               11                 53
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    23  27
  11P LOSS WILD-TYPE 190 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     23   27
  11P LOSS WILD-TYPE  190  209
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               23                190
  MALE                 27                209
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    41   1
  11P LOSS WILD-TYPE 329   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     41    1
  11P LOSS WILD-TYPE  329    8
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                41                329
  YES                1                  8
[1] 2 2
[1] FALSE
D61V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    43   7
  11P LOSS WILD-TYPE 339  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     43    7
  11P LOSS WILD-TYPE  339   55
                               clus
vv                              11P LOSS MUTATED 11P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        43                339
  COLON MUCINOUS ADENOCARCINOMA                7                 55
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    35   0   5   3
  11P LOSS WILD-TYPE 288   4  20  22
D61V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               35                288
  R1                0                  4
  R2                5                 20
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     2
  11P LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           4    23
  11P LOSS WILD-TYPE                        55   189
D61V12, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       4                 55
  WHITE                                          23                189
[1] 4 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
  11P LOSS MUTATED     0  27
  11P LOSS WILD-TYPE   4 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   27
  11P LOSS WILD-TYPE    4  242
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               27                242
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    46  14
  11Q LOSS WILD-TYPE 289  87
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                60                376 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                14                 87 
$`11Q LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3952 
       24.16         6.05        36.00        31.07        12.99         2.01 
TCGA-AA-3972 TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       50.99        43.76        16.57        36.53        32.45        30.44 
TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3666 
       22.52        21.76        23.87         6.97         9.07         2.01 
TCGA-AA-3855 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3968 TCGA-AA-A00Q TCGA-AA-A01F 
       32.05        18.05        24.00        21.99        42.02        32.02 
TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A03J TCGA-AD-6899 
       31.00        33.04         2.96        39.98        40.96         5.79 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D 
       22.42        16.44        14.50         0.95         0.20        17.85 
TCGA-AY-A71X TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-5349 
       19.33         1.41        12.46        12.20         2.01        30.08 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6172 TCGA-CM-6678 
        5.03        15.02        15.02        14.04        11.01        11.01 
TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6924 TCGA-DM-A1D0 
       45.40        20.19        43.27        17.85        14.30       130.65 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A6GC 
       49.91         7.50        61.91        36.00        18.18        12.79 

$`11Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 
       14.93        24.03        29.98        24.00        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       35.11        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        25.18        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 
       35.01        63.98         1.02        38.99         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97        54.02        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       36.03         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
        2.01        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       34.03        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J 
        1.02        26.01        37.02        51.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       83.24        24.53        27.42        26.47         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        16.31        33.01        21.44        17.82        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.39        12.59        12.59        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       13.05        11.08        11.08        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        55.92        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       25.48        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       47.41        35.31       133.18         8.35        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       39.42        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        15.65        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       38.70        60.13        11.90        70.03 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               0.2                0.0 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            130.65             148.01 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            18.755             22.670 
[1] "0.2 - 130.7 (18.8)" "0.0 - 148.0 (22.7)"
[1] "hr=" "1.3"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11Q LOSS MUTATED        11        0        1        15         0         0
  11Q LOSS WILD-TYPE      63        1       28       117        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           4          0          9          6       11
  11Q LOSS WILD-TYPE        16          8         50         35       34
                    vv
clus                 STAGE IVA STAGE IVB
  11Q LOSS MUTATED           3         1
  11Q LOSS WILD-TYPE        14         1
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  11                 63
  STAGE IA                  0                  1
  STAGE II                  1                 28
  STAGE IIA                15                117
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 4                 16
  STAGE IIIA                0                  8
  STAGE IIIB                9                 50
  STAGE IIIC                6                 35
  STAGE IV                 11                 34
  STAGE IVA                 3                 14
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q LOSS MUTATED     3   8  41  10
  11Q LOSS WILD-TYPE   8  69 264  45
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                3                  8
  T2                8                 69
  T3               41                264
  T4               10                 45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  11Q LOSS MUTATED    28  21  13
  11Q LOSS WILD-TYPE 234  84  69
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               28                234
  N1               21                 84
  N2               13                 69
[1] 3 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
  11Q LOSS MUTATED    38  15
  11Q LOSS WILD-TYPE 290  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     38   15
  11Q LOSS WILD-TYPE  290   49
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               38                290
  1               15                 49
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    32  30
  11Q LOSS WILD-TYPE 181 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     32   30
  11Q LOSS WILD-TYPE  181  206
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               32                181
  MALE                 30                206
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    52   1
  11Q LOSS WILD-TYPE 318   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     52    1
  11Q LOSS WILD-TYPE  318    8
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                52                318
  YES                1                  8
[1] 2 2
[1] FALSE
D62V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    53   8
  11Q LOSS WILD-TYPE 329  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     53    8
  11Q LOSS WILD-TYPE  329   54
                               clus
vv                              11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        53                329
  COLON MUCINOUS ADENOCARCINOMA                8                 54
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    43   0   6   3
  11Q LOSS WILD-TYPE 280   4  19  22
D62V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               43                280
  R1                0                  4
  R2                6                 19
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           5    33
  11Q LOSS WILD-TYPE                        54   179
D62V12, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       5                 54
  WHITE                                          33                179
[1] 4 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
  11Q LOSS MUTATED     0  37
  11Q LOSS WILD-TYPE   4 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   37
  11Q LOSS WILD-TYPE    4  232
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               37                232
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    33  15
  12P LOSS WILD-TYPE 302  86
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                48                388 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                15                 86 
$`12P LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 
       24.33        45.60        13.02        24.03         2.01        50.99 
TCGA-CK-5912 TCGA-NH-A8F7 TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 
       49.08        17.85        43.76        34.65        36.53        30.44 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3666 
       20.28        61.84         9.63        26.01        33.99         2.01 
TCGA-AA-3673 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E 
       50.04        31.07        17.03        32.02        33.04         2.96 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AZ-4684 TCGA-CA-5256 TCGA-CM-4750 
        5.79        22.42        16.44        65.00        12.46         8.02 
TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 
        5.03        14.04        29.03        15.02        11.01        11.08 
TCGA-CM-6679 TCGA-D5-6533 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6460 
       10.06        25.48        11.38        12.59         7.50        31.96 
TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-RU-A8FL TCGA-SS-A7HO 
       43.04        65.85        61.91        36.00        38.70        60.13 

$`12P LOSS WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
        0.99        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 
       14.93        31.07        29.98        12.99        24.00        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-3L-AA1B 
       22.09        35.80        26.17        91.79        79.69        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
        4.80        12.66         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 
       16.57        37.05        37.25        37.02        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       56.25         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        9.07        19.07         0.00        29.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 
       61.02        78.08         6.97        54.02        14.01        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       32.05         0.99        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       24.53        27.42        26.47         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 
       21.99        14.99        12.99        13.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        11.01        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        67.30        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       39.42        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        11.90        70.03 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              2.01               0.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             65.85             148.01 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            24.905             21.990 
[1] "2.0 - 65.8 (24.9)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12P LOSS MUTATED         8        0        1         8         2         0
  12P LOSS WILD-TYPE      66        1       28       124         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           2          1          5          9        7
  12P LOSS WILD-TYPE        18          7         54         32       38
                    vv
clus                 STAGE IVA STAGE IVB
  12P LOSS MUTATED           2         0
  12P LOSS WILD-TYPE        15         2
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   8                 66
  STAGE IA                  0                  1
  STAGE II                  1                 28
  STAGE IIA                 8                124
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 2                 18
  STAGE IIIA                1                  7
  STAGE IIIB                5                 54
  STAGE IIIC                9                 32
  STAGE IV                  7                 38
  STAGE IVA                 2                 15
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED     2   7  35   4
  12P LOSS WILD-TYPE   9  70 270  51
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                2                  9
  T2                7                 70
  T3               35                270
  T4                4                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12P LOSS MUTATED    21  14  13
  12P LOSS WILD-TYPE 241  91  69
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               21                241
  N1               14                 91
  N2               13                 69
[1] 3 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
  12P LOSS MUTATED    30   9
  12P LOSS WILD-TYPE 298  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     30    9
  12P LOSS WILD-TYPE  298   55
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               30                298
  1                9                 55
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    24  24
  12P LOSS WILD-TYPE 189 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     24   24
  12P LOSS WILD-TYPE  189  212
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               24                189
  MALE                 24                212
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    42   1
  12P LOSS WILD-TYPE 328   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     42    1
  12P LOSS WILD-TYPE  328    8
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                42                328
  YES                1                  8
[1] 2 2
[1] FALSE
D63V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    47   1
  12P LOSS WILD-TYPE 335  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     47    1
  12P LOSS WILD-TYPE  335   61
                               clus
vv                              12P LOSS MUTATED 12P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        47                335
  COLON MUCINOUS ADENOCARCINOMA                1                 61
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    36   0   3   2
  12P LOSS WILD-TYPE 287   4  22  23
D63V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               36                287
  R1                0                  4
  R2                3                 22
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     1
  12P LOSS WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           6    28
  12P LOSS WILD-TYPE                        53   184
D63V12, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       6                 53
  WHITE                                          28                184
[1] 4 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
  12P LOSS MUTATED     0  31
  12P LOSS WILD-TYPE   4 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   31
  12P LOSS WILD-TYPE    4  238
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               31                238
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    36  14
  12Q LOSS WILD-TYPE 299  87
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                50                386 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                14                 87 
$`12Q LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 
       24.33        45.60        13.02        24.03         2.01        50.99 
TCGA-CK-5912 TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5662 
       49.08        43.76        34.65        36.53        30.44        23.61 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3673 
       20.28        61.84         9.63        26.01        33.99        50.04 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 
       31.07        17.03        32.02        33.04         2.96         5.79 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-CA-5256 TCGA-CA-6716 
       22.42        16.44        14.50         0.20        12.46        12.20 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 
        8.02        29.06         5.03        14.04        29.03        15.02 
TCGA-CM-6172 TCGA-CM-6677 TCGA-D5-6533 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 
       11.01        11.08        25.48        13.41        11.38        12.59 
TCGA-DM-A1DA TCGA-F4-6460 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 
        7.50        31.96        43.04        65.85        61.91        36.00 
TCGA-RU-A8FL TCGA-SS-A7HO 
       38.70        60.13 

$`12Q LOSS WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
        0.99        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 
       14.93        31.07        29.98        12.99        24.00        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       35.11        16.57        37.05        37.25        37.02        32.75 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.45        32.91        31.63        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       56.25         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        9.07        19.07         0.00        29.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       36.03        32.05         0.99        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        10.98        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       83.24        24.53        27.42        26.47         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
       37.02        25.02        26.04        27.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        14.04        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32       140.38        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 
       53.62        44.68        55.04        85.48        39.42        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-T9-A92H TCGA-WS-AB45 
       11.90        70.03 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               0.2                0.0 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             65.85             148.01 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             24.18              21.99 
[1] "0.2 - 65.8 (24.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12Q LOSS MUTATED         8        0        1         8         2         0
  12Q LOSS WILD-TYPE      66        1       28       124         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           1          2          5         10        8
  12Q LOSS WILD-TYPE        19          6         54         31       37
                    vv
clus                 STAGE IVA STAGE IVB
  12Q LOSS MUTATED           2         0
  12Q LOSS WILD-TYPE        15         2
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   8                 66
  STAGE IA                  0                  1
  STAGE II                  1                 28
  STAGE IIA                 8                124
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 19
  STAGE IIIA                2                  6
  STAGE IIIB                5                 54
  STAGE IIIC               10                 31
  STAGE IV                  8                 37
  STAGE IVA                 2                 15
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED     2   8  36   4
  12Q LOSS WILD-TYPE   9  69 269  51
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                2                  9
  T2                8                 69
  T3               36                269
  T4                4                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12Q LOSS MUTATED    21  15  14
  12Q LOSS WILD-TYPE 241  90  68
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               21                241
  N1               15                 90
  N2               14                 68
[1] 3 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
  12Q LOSS MUTATED    31  10
  12Q LOSS WILD-TYPE 297  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     31   10
  12Q LOSS WILD-TYPE  297   54
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               31                297
  1               10                 54
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    26  24
  12Q LOSS WILD-TYPE 187 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     26   24
  12Q LOSS WILD-TYPE  187  212
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               26                187
  MALE                 24                212
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    45   0
  12Q LOSS WILD-TYPE 325   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     45    0
  12Q LOSS WILD-TYPE  325    9
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                45                325
  YES                0                  9
[1] 2 2
[1] FALSE
D64V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    48   2
  12Q LOSS WILD-TYPE 334  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     48    2
  12Q LOSS WILD-TYPE  334   60
                               clus
vv                              12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        48                334
  COLON MUCINOUS ADENOCARCINOMA                2                 60
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    37   0   3   3
  12Q LOSS WILD-TYPE 286   4  22  22
D64V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               37                286
  R1                0                  4
  R2                3                 22
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     2
  12Q LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           5    31
  12Q LOSS WILD-TYPE                        54   181
D64V12, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       5                 54
  WHITE                                          31                181
[1] 4 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
  12Q LOSS MUTATED     0  34
  12Q LOSS WILD-TYPE   4 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   34
  12Q LOSS WILD-TYPE    4  235
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               34                235
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED     8   3
  13Q LOSS WILD-TYPE 327  98
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                11                425 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 98 
$`13Q LOSS MUTATED`
TCGA-AA-3556 TCGA-AZ-4681 TCGA-G4-6314 TCGA-AA-3875 TCGA-AA-A01D TCGA-AU-3779 
       23.01       106.75        35.93        18.05        10.98        14.50 
TCGA-AY-6196 TCGA-AZ-6607 TCGA-CA-5797 TCGA-F4-6704 TCGA-QG-A5Z1 
        0.20         3.19        12.59         1.55         8.42 

$`13Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3560 
       19.07        34.03         0.99        13.02        17.95        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88        75.95       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        17.03        27.02        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       16.44         0.46         0.92        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       18.84       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
        6.77        12.10        29.56         5.23        11.74        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       12.79        16.80        42.77        29.46        32.98        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       21.90        38.70        60.13        11.90        70.03 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               0.2                0.0 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            106.75             148.01 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             12.59              22.09 
[1] "0.2 - 106.8 (12.6)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.5"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  13Q LOSS MUTATED         3        0        0         3         0         0
  13Q LOSS WILD-TYPE      71        1       29       129        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           0          0          1          3        2
  13Q LOSS WILD-TYPE        20          8         58         38       43
                    vv
clus                 STAGE IVA STAGE IVB
  13Q LOSS MUTATED           0         0
  13Q LOSS WILD-TYPE        17         2
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                 71
  STAGE IA                  0                  1
  STAGE II                  0                 29
  STAGE IIA                 3                129
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 20
  STAGE IIIA                0                  8
  STAGE IIIB                1                 58
  STAGE IIIC                3                 38
  STAGE IV                  2                 43
  STAGE IVA                 0                 17
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED     1   2   8   1
  13Q LOSS WILD-TYPE  10  75 297  54
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                1                 10
  T2                2                 75
  T3                8                297
  T4                1                 54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  13Q LOSS MUTATED     6   1   5
  13Q LOSS WILD-TYPE 256 104  77
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                6                256
  N1                1                104
  N2                5                 77
[1] 3 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
  13Q LOSS MUTATED     6   2
  13Q LOSS WILD-TYPE 322  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      6    2
  13Q LOSS WILD-TYPE  322   62
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                6                322
  1                2                 62
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     5   7
  13Q LOSS WILD-TYPE 208 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5    7
  13Q LOSS WILD-TYPE  208  229
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                5                208
  MALE                  7                229
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9   0
  13Q LOSS WILD-TYPE 361   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    0
  13Q LOSS WILD-TYPE  361    9
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 9                361
  YES                0                  9
[1] 2 2
[1] FALSE
D65V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8   3
  13Q LOSS WILD-TYPE 374  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8    3
  13Q LOSS WILD-TYPE  374   59
                               clus
vv                              13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         8                374
  COLON MUCINOUS ADENOCARCINOMA                3                 59
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    10   0   0   1
  13Q LOSS WILD-TYPE 313   4  25  24
D65V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               10                313
  R1                0                  4
  R2                0                 25
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     1
  13Q LOSS WILD-TYPE                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           1     6
  13Q LOSS WILD-TYPE                        58   206
D65V12, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 58
  WHITE                                           6                206
[1] 4 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
  13Q LOSS MUTATED     0   9
  13Q LOSS WILD-TYPE   4 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0    9
  13Q LOSS WILD-TYPE    4  260
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                9                260
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   103  30
  14Q LOSS WILD-TYPE 232  71
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               133                303 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                30                 71 
$`14Q LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       14.53        24.03        19.07        34.03        13.02        23.01 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 
       19.99        19.00        85.05        31.07        24.03        12.99 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AZ-6608 
       50.99        26.01        24.00        38.04        21.99         1.94 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-4N-A93T TCGA-5M-AATE 
       49.08        28.21        91.79        17.85         4.80        39.45 
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       43.76        42.28        35.11        16.57        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6140 
       32.45        32.91        30.44        23.61        22.52        24.13 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        20.61        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3561 
       61.84         5.03         6.97        38.99         9.07        13.94 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3811 
        2.01        14.01        50.04        47.01        37.05        10.06 
TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3866 TCGA-AA-3875 
       25.02        36.95        37.02        17.03        17.03        18.05 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3989 TCGA-AA-A00O TCGA-AA-A00Q 
       21.99        16.08        34.06         7.96        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       14.99        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        2.96         2.01        40.96         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK 
       16.44        14.50         0.95        33.01        17.85        18.84 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 
      109.28         1.41         5.65        22.36        29.56         5.23 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4747 
       12.36        12.46        12.59        12.20         2.01        25.02 
TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
        8.02        17.03        14.04        29.03        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 
       11.08        10.06        45.40        54.61        56.09        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF 
       25.48        15.12        14.30        13.41        11.38        38.20 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A288 TCGA-DM-A28E TCGA-F4-6460 TCGA-F4-6806 
       13.32       140.38        14.04       119.93        31.96        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 
       33.67        13.25         0.53         8.35        82.39        61.91 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-SS-A7HO 
       18.18        19.33        15.65        16.80        38.70        60.13 
TCGA-T9-A92H 
       11.90 

$`14Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        37.05        36.03         8.05         0.99        17.95 
TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         6.05         0.92        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A024 
       14.93        29.98        24.00         2.01        19.07        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
      100.01         5.88        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 
       35.80        26.17        79.69        15.62        12.66         1.61 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 
        9.53        46.65        43.76        43.43        42.90        44.91 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5660 
       37.05        37.25        37.02        32.75        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        25.18        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        56.25         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 
       37.05        35.01        63.98         1.02         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 
       33.99        21.01        24.00        29.95        20.98        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
       78.08         6.97        54.02        47.05        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
        5.98         5.03        26.99        35.05         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       17.98        15.95        38.99         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       53.00        27.02        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 
       26.01        20.98        34.03         2.01        13.05        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        18.05         4.01         0.99        17.03 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02         1.02        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5820 
       18.05        12.16        83.24        24.53        26.47         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 
       17.26        19.33        58.39        32.94         5.13        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 
       62.79        88.21        49.41         6.77        12.10        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
        3.19        12.69        12.39        12.59        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       20.02        37.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       11.08        11.01        12.03        19.59        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.42        17.75        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        26.47        81.37        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6855 
        6.18        47.87         1.55        34.42        43.04        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31       133.18        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A5IV 
       26.04        13.78        46.75        74.79        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        12.79        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       31.30        21.90        70.03 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.53               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            140.38             148.01 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             21.99              22.06 
[1] "0.5 - 140.4 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  14Q LOSS MUTATED        20        0        8        37         2         0
  14Q LOSS WILD-TYPE      54        1       21        95         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           8          4         16          9       19
  14Q LOSS WILD-TYPE        12          4         43         32       26
                    vv
clus                 STAGE IVA STAGE IVB
  14Q LOSS MUTATED          10         0
  14Q LOSS WILD-TYPE         7         2
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  20                 54
  STAGE IA                  0                  1
  STAGE II                  8                 21
  STAGE IIA                37                 95
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 8                 12
  STAGE IIIA                4                  4
  STAGE IIIB               16                 43
  STAGE IIIC                9                 32
  STAGE IV                 19                 26
  STAGE IVA                10                  7
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED     6  21  94  16
  14Q LOSS WILD-TYPE   5  56 211  39
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                6                  5
  T2               21                 56
  T3               94                211
  T4               16                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  14Q LOSS MUTATED    72  40  25
  14Q LOSS WILD-TYPE 190  65  57
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               72                190
  N1               40                 65
  N2               25                 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"
D66V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    93  29
  14Q LOSS WILD-TYPE 235  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     93   29
  14Q LOSS WILD-TYPE  235   35
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               93                235
  1               29                 35
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    64  73
  14Q LOSS WILD-TYPE 149 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     64   73
  14Q LOSS WILD-TYPE  149  163
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               64                149
  MALE                 73                163
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   122   2
  14Q LOSS WILD-TYPE 248   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    122    2
  14Q LOSS WILD-TYPE  248    7
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               122                248
  YES                2                  7
[1] 2 2
[1] FALSE
D66V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   130   3
  14Q LOSS WILD-TYPE 252  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    130    3
  14Q LOSS WILD-TYPE  252   59
                               clus
vv                              14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       130                252
  COLON MUCINOUS ADENOCARCINOMA                3                 59
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    95   0   9   8
  14Q LOSS WILD-TYPE 228   4  16  17
D66V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               95                228
  R1                0                  4
  R2                9                 16
  RX                8                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     4
  14Q LOSS WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          19    62
  14Q LOSS WILD-TYPE                        40   150
D66V12, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                      19                 40
  WHITE                                          62                150
[1] 4 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
  14Q LOSS MUTATED     1  79
  14Q LOSS WILD-TYPE   3 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   79
  14Q LOSS WILD-TYPE    3  190
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               79                190
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   122  31
  15Q LOSS WILD-TYPE 213  70
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               153                283 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                31                 70 
$`15Q LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       24.33        45.60        37.05        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
       19.99        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 
       12.99        50.99        24.00       106.75        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       63.62        91.79         4.80         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       43.76        43.43        44.91        16.57        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 
       32.45        32.91        30.44        29.19        29.16        22.52 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 
       25.08        20.61        21.76        20.28        61.84         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3542 
        7.04         1.02         6.97         9.07        29.00        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3837 
       33.99        21.01         2.01        50.04        37.05        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 
       36.95        37.02        17.03        10.06        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 
       31.07        17.03         2.01        21.99        13.05        34.06 
TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       27.02        19.00        34.03        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        15.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-4070 
       41.00         5.79        22.42        27.42        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4684 
        0.95        33.01         0.20        17.85        18.84        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 
       62.79        88.21        29.56         5.23         3.19        12.46 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 
       12.20        14.30       148.01         2.01        25.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       13.02        29.06         5.03        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       16.04        15.02        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       12.03        20.19        25.48        15.12        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 
        7.53        10.13         9.04        13.41        11.38       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28M 
       92.75        13.32        12.59       140.38       131.51        95.18 
TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       31.96        47.87         1.55        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 
        0.53        47.41         8.35        65.85        55.04        61.91 
TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW 
       36.00        46.75        10.98        19.33        12.79        29.46 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       21.90        38.70        11.90 

$`15Q LOSS WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       17.95         6.05         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       31.07        24.00         2.01        26.01        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 
       75.95       100.01         1.94        28.21        23.51        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       22.09        35.80        26.17        79.69        17.85        15.62 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
       12.66         9.53        46.65        42.90        42.28        35.11 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 
       37.05        37.25        37.02        32.75        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 
       23.61        22.09        22.06        32.71        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
        8.38        25.18        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 
       19.66        16.24        24.92        56.25         9.63         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       37.05        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3553 
       19.07         0.00        29.00        26.01        14.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02        14.01        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 
       25.02         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       33.07         0.00        32.05        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.03        16.08        25.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        0.99        34.98        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
       26.47        16.44         0.46         0.92        27.09        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82        17.26        19.33       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 
        5.65        32.94         5.13        22.36        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       12.10        11.74        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.59        12.76        10.06        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 
       23.05        20.02        37.02        26.04         8.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-5538 
       14.04        11.01        12.95        13.05        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        55.92        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       43.27        17.85         4.80        16.14        15.58        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DA 
       10.26       119.70        24.43        38.20        49.91         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
       44.32       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        8.61        11.11        35.74        35.74         6.18        34.42 
TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       41.42        35.31       133.18        82.39        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 
       53.62        44.68        85.48        39.42        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       13.78        74.79        18.18        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO 
       16.80        42.77        32.98         8.42        31.30        60.13 
TCGA-WS-AB45 
       70.03 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               0.2                0.0 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            148.01             139.17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             21.99              22.06 
[1] "0.2 - 148.0 (22.0)" "0.0 - 139.2 (22.1)"
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  15Q LOSS MUTATED        23        0        7        39         2         0
  15Q LOSS WILD-TYPE      51        1       22        93         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           5          4         18         19       23
  15Q LOSS WILD-TYPE        15          4         41         22       22
                    vv
clus                 STAGE IVA STAGE IVB
  15Q LOSS MUTATED          10         1
  15Q LOSS WILD-TYPE         7         1
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  23                 51
  STAGE IA                  0                  1
  STAGE II                  7                 22
  STAGE IIA                39                 93
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 5                 15
  STAGE IIIA                4                  4
  STAGE IIIB               18                 41
  STAGE IIIC               19                 22
  STAGE IV                 23                 22
  STAGE IVA                10                  7
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED     5  23 111  18
  15Q LOSS WILD-TYPE   6  54 194  37
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                5                  6
  T2               23                 54
  T3              111                194
  T4               18                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  15Q LOSS MUTATED    79  43  35
  15Q LOSS WILD-TYPE 183  62  47
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               79                183
  N1               43                 62
  N2               35                 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"
D67V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   102  34
  15Q LOSS WILD-TYPE 226  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    102   34
  15Q LOSS WILD-TYPE  226   30
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              102                226
  1               34                 30
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    72  85
  15Q LOSS WILD-TYPE 141 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     72   85
  15Q LOSS WILD-TYPE  141  151
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               72                141
  MALE                 85                151
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   132   4
  15Q LOSS WILD-TYPE 238   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    132    4
  15Q LOSS WILD-TYPE  238    5
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               132                238
  YES                4                  5
[1] 2 2
[1] FALSE
D67V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   141  13
  15Q LOSS WILD-TYPE 241  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    141   13
  15Q LOSS WILD-TYPE  241   49
                               clus
vv                              15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       141                241
  COLON MUCINOUS ADENOCARCINOMA               13                 49
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED   109   1  11   7
  15Q LOSS WILD-TYPE 214   3  14  18
D67V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              109                214
  R1                1                  3
  R2               11                 14
  RX                7                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  1     3
  15Q LOSS WILD-TYPE                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                          18    81
  15Q LOSS WILD-TYPE                        41   131
D67V12, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                      18                 41
  WHITE                                          81                131
[1] 4 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
  15Q LOSS MUTATED     2  95
  15Q LOSS WILD-TYPE   2 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   95
  15Q LOSS WILD-TYPE    2  174
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               95                174
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    22   8
  16P LOSS WILD-TYPE 313  93
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                30                406 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 8                 93 
$`16P LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3860 TCGA-A6-3807 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3685 
       14.53        31.07        34.65        21.76        61.84        37.05 
TCGA-AA-3837 TCGA-AA-3966 TCGA-AA-A02W TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       38.99         2.01        41.00        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CM-5344 
       16.31         0.20        17.85         5.65         3.19        22.03 
TCGA-CM-5863 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       15.02        13.02        11.01        11.01        20.19        17.75 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-NH-A50T TCGA-NH-A50U TCGA-RU-A8FL TCGA-T9-A92H 
       49.91         7.50        18.18        10.98        38.70        11.90 

$`16P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       35.11        16.57        37.05        37.25        37.02        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47         0.92        27.09         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       14.04        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       47.41        35.31       133.18         8.35        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       39.42        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       46.75        74.79        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-WS-AB45 
       31.30        21.90        60.13        70.03 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               0.2                0.0 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             61.84             148.01 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            16.375             22.995 
[1] "0.2 - 61.8 (16.4)"  "0.0 - 148.0 (23.0)"
[1] "hr=" "1.6"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16P LOSS MUTATED         3        0        1        11         0         0
  16P LOSS WILD-TYPE      71        1       28       121        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           0          0          6          4        2
  16P LOSS WILD-TYPE        20          8         53         37       43
                    vv
clus                 STAGE IVA STAGE IVB
  16P LOSS MUTATED           4         0
  16P LOSS WILD-TYPE        13         2
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   3                 71
  STAGE IA                  0                  1
  STAGE II                  1                 28
  STAGE IIA                11                121
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 20
  STAGE IIIA                0                  8
  STAGE IIIB                6                 53
  STAGE IIIC                4                 37
  STAGE IV                  2                 43
  STAGE IVA                 4                 13
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED     0   3  23   5
  16P LOSS WILD-TYPE  11  74 282  50
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                 11
  T2                3                 74
  T3               23                282
  T4                5                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  16P LOSS MUTATED    16   8   7
  16P LOSS WILD-TYPE 246  97  75
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               16                246
  N1                8                 97
  N2                7                 75
[1] 3 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
  16P LOSS MUTATED    19   6
  16P LOSS WILD-TYPE 309  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     19    6
  16P LOSS WILD-TYPE  309   58
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               19                309
  1                6                 58
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    16  15
  16P LOSS WILD-TYPE 197 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     16   15
  16P LOSS WILD-TYPE  197  221
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               16                197
  MALE                 15                221
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    25   0
  16P LOSS WILD-TYPE 345   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     25    0
  16P LOSS WILD-TYPE  345    9
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                25                345
  YES                0                  9
[1] 2 2
[1] FALSE
D68V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    25   6
  16P LOSS WILD-TYPE 357  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     25    6
  16P LOSS WILD-TYPE  357   56
                               clus
vv                              16P LOSS MUTATED 16P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        25                357
  COLON MUCINOUS ADENOCARCINOMA                6                 56
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    22   1   0   1
  16P LOSS WILD-TYPE 301   3  25  24
D68V10, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               22                301
  R1                1                  3
  R2                0                 25
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           9    17
  16P LOSS WILD-TYPE                        50   195
D68V12, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       9                 50
  WHITE                                          17                195
[1] 4 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
  16P LOSS MUTATED     1  24
  16P LOSS WILD-TYPE   3 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   24
  16P LOSS WILD-TYPE    3  245
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               24                245
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    21   6
  16Q LOSS WILD-TYPE 314  95
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                27                409 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                 95 
$`16Q LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3860 TCGA-A6-3807 TCGA-A6-6651 TCGA-AA-3494 TCGA-AA-3685 
       14.53        31.07        34.65        21.76         1.02        37.05 
TCGA-AA-3837 TCGA-AA-3966 TCGA-AA-A02W TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-6196 
       38.99         2.01        41.00        16.44        16.31         0.20 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-6169 
       17.85         5.65         3.19        22.03        15.02        13.02 
TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-DM-A1DA TCGA-NH-A50T 
       11.01        11.01        20.19        17.75         7.50        18.18 
TCGA-NH-A50U TCGA-RU-A8FL TCGA-T9-A92H 
       10.98        38.70        11.90 

$`16Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       35.11        16.57        37.05        37.25        37.02        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        5.03         7.04         3.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        33.01        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.42        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V 
       26.43        26.04        13.78        46.75        74.79        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        21.90        60.13 
TCGA-WS-AB45 
       70.03 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               0.2                0.0 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             41.00             148.01 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             16.31              23.01 
[1] "0.2 - 41.0 (16.3)"  "0.0 - 148.0 (23.0)"
[1] "hr=" "1.5"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16Q LOSS MUTATED         3        0        1         9         0         0
  16Q LOSS WILD-TYPE      71        1       28       123        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           0          0          6          4        2
  16Q LOSS WILD-TYPE        20          8         53         37       43
                    vv
clus                 STAGE IVA STAGE IVB
  16Q LOSS MUTATED           3         0
  16Q LOSS WILD-TYPE        14         2
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   3                 71
  STAGE IA                  0                  1
  STAGE II                  1                 28
  STAGE IIA                 9                123
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 20
  STAGE IIIA                0                  8
  STAGE IIIB                6                 53
  STAGE IIIC                4                 37
  STAGE IV                  2                 43
  STAGE IVA                 3                 14
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED     0   3  21   4
  16Q LOSS WILD-TYPE  11  74 284  51
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                 11
  T2                3                 74
  T3               21                284
  T4                4                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  16Q LOSS MUTATED    15   7   6
  16Q LOSS WILD-TYPE 247  98  76
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               15                247
  N1                7                 98
  N2                6                 76
[1] 3 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
  16Q LOSS MUTATED    17   5
  16Q LOSS WILD-TYPE 311  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     17    5
  16Q LOSS WILD-TYPE  311   59
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               17                311
  1                5                 59
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    14  14
  16Q LOSS WILD-TYPE 199 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     14   14
  16Q LOSS WILD-TYPE  199  222
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               14                199
  MALE                 14                222
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    23   0
  16Q LOSS WILD-TYPE 347   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     23    0
  16Q LOSS WILD-TYPE  347    9
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                23                347
  YES                0                  9
[1] 2 2
[1] FALSE
D69V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    23   5
  16Q LOSS WILD-TYPE 359  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     23    5
  16Q LOSS WILD-TYPE  359   57
                               clus
vv                              16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        23                359
  COLON MUCINOUS ADENOCARCINOMA                5                 57
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    20   1   1   1
  16Q LOSS WILD-TYPE 303   3  24  24
D69V10, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               20                303
  R1                1                  3
  R2                1                 24
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           8    14
  16Q LOSS WILD-TYPE                        51   198
D69V12, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       8                 51
  WHITE                                          14                198
[1] 4 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
  16Q LOSS MUTATED     1  21
  16Q LOSS WILD-TYPE   3 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   21
  16Q LOSS WILD-TYPE    3  248
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               21                248
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   169  59
  17P LOSS WILD-TYPE 166  42
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               228                208 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                59                 42 
$`17P LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       36.03        13.02        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3952 
       19.00        36.00        85.05        24.03        29.98         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 
       50.99        26.01        24.00        38.04        21.99        21.37 
TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 
       15.52       106.75         1.94        49.08         5.88        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-5M-AAT4 TCGA-5M-AATE 
       63.62        35.93        91.79        17.85         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.76        43.43        42.28        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        34.65        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       30.44        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 
       25.18        20.61        23.87        20.28        61.84         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        7.04         1.02        37.05         6.97        38.99         9.07 
TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       29.00        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02        78.08         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3837 
       47.01         5.98        37.05        10.06        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
       36.95        37.02        10.06        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       31.07        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D 
       20.98        34.03        16.08        27.02         7.96        19.00 
TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01C 
       34.03        27.02        42.02        17.03        14.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z 
       10.98        32.02        12.00         1.02        33.04        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J 
        2.96        39.98         2.01         5.03        41.00        40.96 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46        14.50        16.31         0.95        33.01         0.20 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 
       17.85       109.28         1.41         5.65         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       65.00        88.21        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 
       12.69        12.46        12.59        12.20        14.30        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        2.01        25.02         8.02        27.02        13.02        29.06 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
        5.03        15.02        17.03        29.03        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       13.02        15.02        11.01        13.05        11.08        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 
       45.40        54.61        19.59        56.09        55.92        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       18.25        25.48        43.27        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 
        7.53        10.13        12.43        14.30         9.04        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      140.38        44.32       131.51       139.17        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6805 
      119.93        35.97       117.07        31.96        11.11        34.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6306 
       43.04        33.67        13.25         8.35        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A50U 
       55.04        39.42        61.91        26.43        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        21.90        38.70        60.13        11.90 

$`17P LOSS WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3530 
       45.60        13.94        58.03        13.02         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 
       34.03         0.99        17.95         0.92        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A024 
       14.93        31.07        12.99        24.00        19.07        39.06 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6321 
       25.08        10.88        75.95       100.01        28.21        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       35.80        26.17        79.69        15.62         4.80        12.66 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3809 
        9.53        46.65        42.90        44.91        37.02        32.75 
TCGA-A6-3810 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       36.53        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
        8.38        25.08        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 
       19.66        16.24        24.92        56.25         9.63         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
       35.01        63.98         1.02         1.02        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 
       29.00        26.01        29.95        20.98         6.97        54.02 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       47.05        15.02        11.01         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3846 
        0.99         1.02        17.98        15.95         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
        0.00         0.00        36.03        53.00        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       26.01         2.01        21.99        13.05        34.06        25.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01K 
        4.01         0.99        34.98        15.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 
       38.07         1.02        35.01         1.02        26.01        51.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
        0.92        22.03        39.98        18.05        12.16        83.24 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.92        27.09        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
       18.84        58.39        32.94        62.79        49.41         6.77 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       11.74        12.36        12.39        12.59        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       26.04        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6168 
       15.02        15.02        12.00        14.04        16.04        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 
       14.04        12.95        11.08        11.01        12.03        20.19 
TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 
       20.42        15.12        17.85         4.80        16.14        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.44        11.64        13.41        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C 
      119.70        49.91         7.50       135.65         7.76        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 
       60.79        98.24        95.18         8.61        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6854 TCGA-F4-6855 
        6.18        47.87         1.55        41.42         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       35.31       133.18        82.39        74.56        67.30        53.62 
TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T 
       85.48        36.00        26.04        13.78        74.79        18.18 
TCGA-NH-A5IV TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 
       19.33        29.46        31.30        70.03 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               0.2                0.0 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            140.38             148.01 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             23.26              21.60 
[1] "0.2 - 140.4 (23.3)" "0.0 - 148.0 (21.6)"
[1] "hr=" "1.3"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17P LOSS MUTATED        32        0       14        55         2         1
  17P LOSS WILD-TYPE      42        1       15        77         8         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED          10          8         30         27       33
  17P LOSS WILD-TYPE        10          0         29         14       12
                    vv
clus                 STAGE IVA STAGE IVB
  17P LOSS MUTATED          12         2
  17P LOSS WILD-TYPE         5         0
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  32                 42
  STAGE IA                  0                  1
  STAGE II                 14                 15
  STAGE IIA                55                 77
  STAGE IIB                 2                  8
  STAGE IIC                 1                  0
  STAGE III                10                 10
  STAGE IIIA                8                  0
  STAGE IIIB               30                 29
  STAGE IIIC               27                 14
  STAGE IV                 33                 12
  STAGE IVA                12                  5
  STAGE IVB                 2                  0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED     7  36 161  30
  17P LOSS WILD-TYPE   4  41 144  25
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                7                  4
  T2               36                 41
  T3              161                144
  T4               30                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  17P LOSS MUTATED   116  64  54
  17P LOSS WILD-TYPE 146  41  28
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              116                146
  N1               64                 41
  N2               54                 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"
D70V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   160  47
  17P LOSS WILD-TYPE 168  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    160   47
  17P LOSS WILD-TYPE  168   17
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              160                168
  1               47                 17
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   100 134
  17P LOSS WILD-TYPE 113 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    100  134
  17P LOSS WILD-TYPE  113  102
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              100                113
  MALE                134                102
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   193   5
  17P LOSS WILD-TYPE 177   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    193    5
  17P LOSS WILD-TYPE  177    4
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               193                177
  YES                5                  4
[1] 2 2
[1] FALSE
D70V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   216  14
  17P LOSS WILD-TYPE 166  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    216   14
  17P LOSS WILD-TYPE  166   48
                               clus
vv                              17P LOSS MUTATED 17P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       216                166
  COLON MUCINOUS ADENOCARCINOMA               14                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   163   2  17   8
  17P LOSS WILD-TYPE 160   2   8  17
D70V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              163                160
  R1                2                  2
  R2               17                  8
  RX                8                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     5
  17P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                          31   112
  17P LOSS WILD-TYPE                        28   100
D70V12, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                  6
  BLACK OR AFRICAN AMERICAN                      31                 28
  WHITE                                         112                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     2 139
  17P LOSS WILD-TYPE   2 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2  139
  17P LOSS WILD-TYPE    2  130
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO              139                130
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    45  18
  17Q LOSS WILD-TYPE 290  83
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                63                373 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                18                 83 
$`17Q LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3976 TCGA-CK-5912 
       24.16        24.03        19.99         6.05        26.01        49.08 
TCGA-G4-6314 TCGA-NH-A8F7 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4107 
       35.93        17.85        43.76        43.76        37.05        32.45 
TCGA-AA-3495 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 
       37.05        12.99        21.01         2.01        50.04        37.05 
TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3989 TCGA-AA-A00F 
       10.06        37.02        27.02        24.00         7.96        34.03 
TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E 
       42.02        10.98        32.02        33.04        37.02         2.96 
TCGA-AA-A02F TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-6196 
       39.98         5.79        22.42        26.47        14.50         0.20 
TCGA-AY-A69D TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4751 TCGA-CM-4752 
       17.85        12.10        12.59        12.20        27.02        13.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-D5-5537 TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6924 
        5.03        15.02        45.40        43.27        12.49        14.30 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-F4-6460 TCGA-F4-6704 
       11.38        38.20        12.59       140.38        31.96         1.55 
TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6320 TCGA-NH-A50U TCGA-NH-A6GB TCGA-NH-A6GC 
       13.25         8.35        26.43        10.98        15.65        12.79 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QL-A97D 
       42.77        32.98        21.90 

$`17Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3672 
        0.99        13.02        17.95        23.01        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       50.99        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
      100.01         1.94         5.88        28.21        23.51        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-3L-AA1B 
       22.09        35.80        26.17        91.79        79.69        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
        4.80        12.66         1.61         9.53        39.45        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       37.25        37.02        34.65        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 
       29.00        26.01        14.01        33.99        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        36.95         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 
        0.99        31.07        53.00        17.03        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        15.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       51.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
       27.42        16.44         0.46         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        33.01        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       18.84       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.46        12.39        12.59        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.41        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA 
       24.43       130.65        92.75        49.91        13.32         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        43.04        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 
        0.53        47.41        35.31       133.18        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       39.42        61.91        36.00        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 
       74.79        18.18        19.33        19.33         9.93        16.80 
TCGA-QG-A5YW TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       29.46         8.42        31.30        38.70        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               0.2                0.0 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            140.38             148.01 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             22.42              22.03 
[1] "0.2 - 140.4 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17Q LOSS MUTATED         7        0        5        12         0         0
  17Q LOSS WILD-TYPE      67        1       24       120        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           4          2          6         11        9
  17Q LOSS WILD-TYPE        16          6         53         30       36
                    vv
clus                 STAGE IVA STAGE IVB
  17Q LOSS MUTATED           4         1
  17Q LOSS WILD-TYPE        13         1
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   7                 67
  STAGE IA                  0                  1
  STAGE II                  5                 24
  STAGE IIA                12                120
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 4                 16
  STAGE IIIA                2                  6
  STAGE IIIB                6                 53
  STAGE IIIC               11                 30
  STAGE IV                  9                 36
  STAGE IVA                 4                 13
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED     0   9  45  10
  17Q LOSS WILD-TYPE  11  68 260  45
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                 11
  T2                9                 68
  T3               45                260
  T4               10                 45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  17Q LOSS MUTATED    26  20  18
  17Q LOSS WILD-TYPE 236  85  64
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               26                236
  N1               20                 85
  N2               18                 64
[1] 3 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
  17Q LOSS MUTATED    36  14
  17Q LOSS WILD-TYPE 292  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     36   14
  17Q LOSS WILD-TYPE  292   50
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               36                292
  1               14                 50
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    30  34
  17Q LOSS WILD-TYPE 183 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     30   34
  17Q LOSS WILD-TYPE  183  202
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               30                183
  MALE                 34                202
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    54   2
  17Q LOSS WILD-TYPE 316   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     54    2
  17Q LOSS WILD-TYPE  316    7
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                54                316
  YES                2                  7
[1] 2 2
[1] FALSE
D71V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    55   8
  17Q LOSS WILD-TYPE 327  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     55    8
  17Q LOSS WILD-TYPE  327   54
                               clus
vv                              17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        55                327
  COLON MUCINOUS ADENOCARCINOMA                8                 54
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    45   1   5   4
  17Q LOSS WILD-TYPE 278   3  20  21
D71V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               45                278
  R1                1                  3
  R2                5                 20
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  1     2
  17Q LOSS WILD-TYPE                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                          10    28
  17Q LOSS WILD-TYPE                        49   184
D71V12, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      10                 49
  WHITE                                          28                184
[1] 4 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
  17Q LOSS MUTATED     0  38
  17Q LOSS WILD-TYPE   4 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   38
  17Q LOSS WILD-TYPE    4  231
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               38                231
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   190  55
  18P LOSS WILD-TYPE 145  46
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               245                191 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                55                 46 
$`18P LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3522 
       24.33        45.60        13.94        14.53         1.02        37.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       19.07        34.03        13.02        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        6.05        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       24.03        29.98        12.99        50.99        26.01        24.00 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       38.04        21.99        15.52       106.75         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-NH-A8F7 TCGA-3L-AA1B 
       28.21        23.51        63.62        35.93        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
        4.80        12.66         1.61        39.45        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.43        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       37.25        34.65        36.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       29.19        23.61        22.09        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       24.13        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        7.04         1.02        37.05         6.97        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       19.07        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 
       24.00        13.94        61.02        78.08         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3837 
       50.04        47.01        15.02        37.05        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       36.95        37.02        17.03        10.06        33.07         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 
       31.07        17.03        27.02        18.05        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
       34.03        21.99        16.08        13.05        34.06        27.02 
TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W 
        7.96        19.00        34.03        27.02        42.02        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       15.02        15.02        32.02        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       26.01         2.96        39.98         2.01         5.03        41.00 
TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D 
       16.44        14.50         0.95        33.01        17.26        17.85 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       18.84       109.28         5.65         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5256 
       62.79        12.10        29.56         5.23        12.69        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 
       12.59        12.59        12.20        14.30        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       25.02         8.02        13.02        29.06        22.03        30.08 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 
       21.99        13.02        15.02        11.01        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        54.61        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       20.19        18.25        25.48        17.85        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
        7.53        12.43        14.30         9.04        13.41        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      140.38        44.32       139.17        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       35.97       117.07        95.18         8.61        31.96        11.11 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 
       13.25         0.53        47.41         8.35        82.39        65.85 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       55.04        61.91        36.00        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       10.98        19.33        12.79        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        21.90        38.70        60.13        11.90 

$`18P LOSS WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       24.16        58.03        13.02        24.03        36.03         8.05 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 
        0.99        17.95         0.92        19.04        19.04        24.00 
TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
        2.01        19.07        39.06        21.37        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       75.95       100.01         5.88        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2686 
       91.79        79.69         9.53        46.65        42.90        37.02 
TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 
       32.75        31.63        33.53        22.06        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 
       25.08        20.12        19.66        16.24        24.92         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3534 
       35.01        63.98         1.02         1.02         0.00        29.00 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 
       21.01        29.95        20.98         6.97        54.02        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 
        0.99         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 
        0.00        36.03        32.05        53.00        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 
       33.01        26.01         2.01        25.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       38.04        30.02        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       17.03        34.98        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O 
        1.02        35.01         1.02        37.02        51.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5820 
       22.03        39.98        18.05        12.16        83.24         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31         0.20        21.44        17.82 
TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6598 
       19.33        58.39         1.41        32.94        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
        6.77        11.74         3.19        12.36        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       37.02        26.04        27.02        22.98        32.02        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       15.02        15.02        12.00        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6531 
       12.95        13.05        11.08        19.59        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       43.27        15.12         4.80        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       10.13         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      119.70        92.75         7.50       131.51       135.65         7.76 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       81.37        60.79        98.24        35.74         6.18        47.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        67.30        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV 
       85.48        39.42        26.43        26.04        13.78        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 
        9.93        15.65        29.46        31.30        70.03 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.53               0.00 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            140.38             148.01 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             23.61              20.98 
[1] "0.5 - 140.4 (23.6)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1"  
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18P LOSS MUTATED        37        0       12        66         3         1
  18P LOSS WILD-TYPE      37        1       17        66         7         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED           8          6         35         25       35
  18P LOSS WILD-TYPE        12          2         24         16       10
                    vv
clus                 STAGE IVA STAGE IVB
  18P LOSS MUTATED          15         1
  18P LOSS WILD-TYPE         2         1
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  37                 37
  STAGE IA                  0                  1
  STAGE II                 12                 17
  STAGE IIA                66                 66
  STAGE IIB                 3                  7
  STAGE IIC                 1                  0
  STAGE III                 8                 12
  STAGE IIIA                6                  2
  STAGE IIIB               35                 24
  STAGE IIIC               25                 16
  STAGE IV                 35                 10
  STAGE IVA                15                  2
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED     7  41 172  31
  18P LOSS WILD-TYPE   4  36 133  24
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                7                  4
  T2               41                 36
  T3              172                133
  T4               31                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  18P LOSS MUTATED   131  68  52
  18P LOSS WILD-TYPE 131  37  30
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0              131                131
  N1               68                 37
  N2               52                 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"
D72V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   170  51
  18P LOSS WILD-TYPE 158  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    170   51
  18P LOSS WILD-TYPE  158   13
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              170                158
  1               51                 13
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   114 137
  18P LOSS WILD-TYPE  99  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    114  137
  18P LOSS WILD-TYPE   99   99
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              114                 99
  MALE                137                 99
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   213   5
  18P LOSS WILD-TYPE 157   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    213    5
  18P LOSS WILD-TYPE  157    4
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO               213                157
  YES                5                  4
[1] 2 2
[1] FALSE
D72V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   236  11
  18P LOSS WILD-TYPE 146  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    236   11
  18P LOSS WILD-TYPE  146   51
                               clus
vv                              18P LOSS MUTATED 18P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       236                146
  COLON MUCINOUS ADENOCARCINOMA               11                 51
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED   176   1  18  11
  18P LOSS WILD-TYPE 147   3   7  14
D72V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              176                147
  R1                1                  3
  R2               18                  7
  RX               11                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  1     6
  18P LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          36   119
  18P LOSS WILD-TYPE                        23    93
D72V12, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           6                  5
  BLACK OR AFRICAN AMERICAN                      36                 23
  WHITE                                         119                 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"
D72V13, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3 151
  18P LOSS WILD-TYPE   1 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3  151
  18P LOSS WILD-TYPE    1  118
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO              151                118
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   200  61
  18Q LOSS WILD-TYPE 135  40
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               261                175 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                61                 40 
$`18Q LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        13.94        14.53         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       37.05        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 
       50.99        26.01        24.00        21.99        15.52       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       35.93        91.79        17.85        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        1.61        39.45        43.76        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       29.19        23.61        32.71        29.16        27.09        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       25.18        20.61        21.76        24.39        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       61.84        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 
       37.05         6.97        38.99         9.07        19.07        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3561 
       26.01        12.99        14.01        33.99        24.00        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       61.02        78.08         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       15.02        37.05        25.02        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03        10.06        33.07         0.99        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       27.02        18.05        24.00        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D 
       16.08        13.05        34.06        27.02         7.96        19.00 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       34.03        42.02        17.03        14.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       10.98        32.02        31.00         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       37.02         2.96        39.98         2.01         5.03        41.00 
TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L 
       16.44         0.46        14.50        16.31        33.01        17.26 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 
       17.85        18.84       109.28         5.65         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        88.21        12.10        29.56         5.23 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.69        12.46        12.59        12.59        12.20        14.30 
TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
      148.01        21.99         2.01        25.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 
       13.02        29.06        22.03        30.08         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
       17.03        14.04        29.03        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        11.01        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       20.19        18.25        25.48        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
       15.58         7.53        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 
       13.32        12.59       140.38         7.50        44.32       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
       14.04        26.47       119.93       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        11.11        35.74         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
       43.04        13.25         0.53        47.41         8.35        82.39 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        39.42        61.91        36.00 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       46.75        74.79        18.18        10.98        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       12.79        16.80        42.77        32.98         8.42        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       38.70        60.13        11.90 

$`18Q LOSS WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       24.16        58.03        13.02         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00L 
        0.92        19.04        19.04        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 
       39.06        21.37        25.08        10.88        75.95       100.01 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-5M-AAT6 TCGA-A6-2672 
       22.09        35.80        26.17        79.69         9.53        46.65 
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 
       42.90        32.75        33.53        22.09        22.06        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        25.08        24.69        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
       24.92         3.02        35.01        63.98         1.02         1.02 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 
        0.00        29.00        21.01        29.95        20.98         6.97 
TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       54.02        47.05        11.01         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
        0.00         0.00         0.00        36.03        32.05        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 
       31.00         2.01        33.01        26.01         2.01        25.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I 
        4.01        27.02         0.99        34.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02O 
       38.07         1.02        35.01         1.02        51.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5821 
       22.03        39.98        18.05        12.16        83.24         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X 
       27.09         0.95         0.20        21.44        17.82        19.33 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 
       58.39         1.41        32.94        49.41         6.77        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.19        12.36        12.39        12.76        10.06        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        70.16        15.62        51.32        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 
      124.27        23.05        20.02        37.02        26.04        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 
       32.02        15.02        15.02        15.02        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6530 TCGA-D5-6531 
       12.99        14.04        12.95        13.05        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6922 
       43.27        15.12         4.80        16.14        12.39        10.13 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65         7.76        81.37        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 TCGA-F4-6856 
       98.24        35.74         6.18        47.87        33.67        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
      133.18        74.56        67.30        53.62        85.48        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 
       26.04        13.78        19.33        15.65        29.46        31.30 
TCGA-WS-AB45 
       70.03 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.46               0.00 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            148.01             135.65 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             23.51              21.14 
[1] "0.5 - 148.0 (23.5)" "0.0 - 135.7 (21.1)"
[1] "hr=" "1"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18Q LOSS MUTATED        37        0       15        69         3         1
  18Q LOSS WILD-TYPE      37        1       14        63         7         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED          10          7         37         28       36
  18Q LOSS WILD-TYPE        10          1         22         13        9
                    vv
clus                 STAGE IVA STAGE IVB
  18Q LOSS MUTATED          15         1
  18Q LOSS WILD-TYPE         2         1
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  37                 37
  STAGE IA                  0                  1
  STAGE II                 15                 14
  STAGE IIA                69                 63
  STAGE IIB                 3                  7
  STAGE IIC                 1                  0
  STAGE III                10                 10
  STAGE IIIA                7                  1
  STAGE IIIB               37                 22
  STAGE IIIC               28                 13
  STAGE IV                 36                  9
  STAGE IVA                15                  2
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q LOSS MUTATED     6  43 186  32
  18Q LOSS WILD-TYPE   5  34 119  23
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                6                  5
  T2               43                 34
  T3              186                119
  T4               32                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  18Q LOSS MUTATED   137  73  57
  18Q LOSS WILD-TYPE 125  32  25
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              137                125
  N1               73                 32
  N2               57                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   185  52
  18Q LOSS WILD-TYPE 143  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    185   52
  18Q LOSS WILD-TYPE  143   12
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              185                143
  1               52                 12
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   121 146
  18Q LOSS WILD-TYPE  92  90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    121  146
  18Q LOSS WILD-TYPE   92   90
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              121                 92
  MALE                146                 90
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   225   5
  18Q LOSS WILD-TYPE 145   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    225    5
  18Q LOSS WILD-TYPE  145    4
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               225                145
  YES                5                  4
[1] 2 2
[1] FALSE
D73V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   250  14
  18Q LOSS WILD-TYPE 132  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    250   14
  18Q LOSS WILD-TYPE  132   48
                               clus
vv                              18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       250                132
  COLON MUCINOUS ADENOCARCINOMA               14                 48
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   190   2  18  11
  18Q LOSS WILD-TYPE 133   2   7  14
D73V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              190                133
  R1                2                  2
  R2               18                  7
  RX               11                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  1     6
  18Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          37   130
  18Q LOSS WILD-TYPE                        22    82
D73V12, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           6                  5
  BLACK OR AFRICAN AMERICAN                      37                 22
  WHITE                                         130                 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"
D73V13, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3 163
  18Q LOSS WILD-TYPE   1 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3  163
  18Q LOSS WILD-TYPE    1  106
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO              163                106
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    26  13
  19P LOSS WILD-TYPE 309  88
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                39                397 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                 88 
$`19P LOSS MUTATED`
TCGA-AA-3506 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3692 TCGA-AA-3867 
       58.03        13.02        23.01        19.99        36.00        24.03 
TCGA-AA-3952 TCGA-CK-5912 TCGA-DM-A285 TCGA-A6-3807 TCGA-A6-6142 TCGA-A6-A567 
        2.01        49.08         5.88        34.65        25.08        61.84 
TCGA-AA-3538 TCGA-AA-3666 TCGA-AA-3866 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A01D 
       26.01         2.01        17.03        24.00         2.01        10.98 
TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W TCGA-AY-6196 
       12.00        33.04        26.01        39.98        41.00         0.20 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-CA-5797 TCGA-CK-4948 TCGA-CM-6675 TCGA-D5-5537 
        5.13        65.00        12.59       148.01        13.05        45.40 
TCGA-D5-6533 TCGA-D5-6537 TCGA-DM-A1DB TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6317 
       25.48         4.80        44.32        33.67         8.35        36.00 
TCGA-NH-A50U TCGA-RU-A8FL TCGA-SS-A7HO 
       10.98        38.70        60.13 

$`19P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 
       34.03         0.99        17.95        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99        24.00        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4N-A93T 
       26.17        91.79        79.69        17.85        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.05        37.25        37.02        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       22.52        24.13         8.38        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
        0.99        31.07        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
        2.01        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
        1.02        37.02        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       54.61        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       26.04        13.78        46.75        74.79        18.18        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       29.46        32.98         8.42        31.30        21.90        11.90 
TCGA-WS-AB45 
       70.03 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               0.2                0.0 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            148.01             140.38 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             25.08              21.99 
[1] "0.2 - 148.0 (25.1)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.5"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19P LOSS MUTATED         7        0        1         5         1         0
  19P LOSS WILD-TYPE      67        1       28       127         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           4          0          2          7        7
  19P LOSS WILD-TYPE        16          8         57         34       38
                    vv
clus                 STAGE IVA STAGE IVB
  19P LOSS MUTATED           4         1
  19P LOSS WILD-TYPE        13         1
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   7                 67
  STAGE IA                  0                  1
  STAGE II                  1                 28
  STAGE IIA                 5                127
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 4                 16
  STAGE IIIA                0                  8
  STAGE IIIB                2                 57
  STAGE IIIC                7                 34
  STAGE IV                  7                 38
  STAGE IVA                 4                 13
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED     1   7  27   5
  19P LOSS WILD-TYPE  10  70 278  50
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                 10
  T2                7                 70
  T3               27                278
  T4                5                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  19P LOSS MUTATED    15   9  16
  19P LOSS WILD-TYPE 247  96  66
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               15                247
  N1                9                 96
  N2               16                 66
[1] 3 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
  19P LOSS MUTATED    22  12
  19P LOSS WILD-TYPE 306  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     22   12
  19P LOSS WILD-TYPE  306   52
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               22                306
  1               12                 52
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    20  20
  19P LOSS WILD-TYPE 193 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     20   20
  19P LOSS WILD-TYPE  193  216
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               20                193
  MALE                 20                216
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    32   1
  19P LOSS WILD-TYPE 338   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     32    1
  19P LOSS WILD-TYPE  338    8
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                32                338
  YES                1                  8
[1] 2 2
[1] FALSE
D74V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    32   7
  19P LOSS WILD-TYPE 350  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     32    7
  19P LOSS WILD-TYPE  350   55
                               clus
vv                              19P LOSS MUTATED 19P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        32                350
  COLON MUCINOUS ADENOCARCINOMA                7                 55
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    25   0   4   3
  19P LOSS WILD-TYPE 298   4  21  22
D74V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               25                298
  R1                0                  4
  R2                4                 21
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     1
  19P LOSS WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           5    15
  19P LOSS WILD-TYPE                        54   197
D74V12, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       5                 54
  WHITE                                          15                197
[1] 4 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
  19P LOSS MUTATED     0  20
  19P LOSS WILD-TYPE   4 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   20
  19P LOSS WILD-TYPE    4  249
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               20                249
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    22  10
  19Q LOSS WILD-TYPE 313  91
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                32                404 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                10                 91 
$`19Q LOSS MUTATED`
TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3692 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-A00Z 
       23.01        19.99        36.00        24.03         2.01        21.99 
TCGA-CK-5912 TCGA-DM-A285 TCGA-A6-3807 TCGA-AA-3538 TCGA-AA-3666 TCGA-AA-3866 
       49.08         5.88        34.65        26.01         2.01        17.03 
TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A004 TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X 
       24.00         2.01        13.94        10.98        33.04        26.01 
TCGA-AA-A02W TCGA-AZ-4616 TCGA-AZ-4684 TCGA-CK-4948 TCGA-CM-6675 TCGA-D5-5537 
       41.00         5.13        65.00       148.01        13.05        45.40 
TCGA-D5-6533 TCGA-DM-A1DB TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6317 
       25.48        44.32         1.55        33.67         8.35        36.00 
TCGA-NH-A50U TCGA-RU-A8FL 
       10.98        38.70 

$`19Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3560 
       19.07        34.03         0.99        13.02        17.95        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        19.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 
       14.93        31.07        29.98        12.99        24.00        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 TCGA-AD-6548 
       26.01        24.00        19.07        38.04        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        1.94        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       35.80        26.17        91.79        79.69        17.85        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       35.11        16.57        37.05        37.25        37.02        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        9.07        19.07         0.00        29.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       25.02        27.02         7.96        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02         1.02        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       18.84       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       54.61        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       17.75        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38         7.50       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       26.04        13.78        46.75        74.79        18.18        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        21.90        60.13 
TCGA-T9-A92H TCGA-WS-AB45 
       11.90        70.03 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1.55               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            148.01             140.38 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            24.015             22.010 
[1] "1.6 - 148.0 (24.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.5"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19Q LOSS MUTATED         6        0        1         5         0         0
  19Q LOSS WILD-TYPE      68        1       28       127        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           4          0          1          6        5
  19Q LOSS WILD-TYPE        16          8         58         35       40
                    vv
clus                 STAGE IVA STAGE IVB
  19Q LOSS MUTATED           3         1
  19Q LOSS WILD-TYPE        14         1
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   6                 68
  STAGE IA                  0                  1
  STAGE II                  1                 28
  STAGE IIA                 5                127
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 4                 16
  STAGE IIIA                0                  8
  STAGE IIIB                1                 58
  STAGE IIIC                6                 35
  STAGE IV                  5                 40
  STAGE IVA                 3                 14
  STAGE IVB                 1                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED     1   6  22   4
  19Q LOSS WILD-TYPE  10  71 283  51
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                 10
  T2                6                 71
  T3               22                283
  T4                4                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  19Q LOSS MUTATED    13   5  15
  19Q LOSS WILD-TYPE 249 100  67
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               13                249
  N1                5                100
  N2               15                 67
[1] 3 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
  19Q LOSS MUTATED    19   9
  19Q LOSS WILD-TYPE 309  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     19    9
  19Q LOSS WILD-TYPE  309   55
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               19                309
  1                9                 55
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    17  16
  19Q LOSS WILD-TYPE 196 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     17   16
  19Q LOSS WILD-TYPE  196  220
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               17                196
  MALE                 16                220
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    25   1
  19Q LOSS WILD-TYPE 345   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     25    1
  19Q LOSS WILD-TYPE  345    8
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                25                345
  YES                1                  8
[1] 2 2
[1] FALSE
D75V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    26   6
  19Q LOSS WILD-TYPE 356  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     26    6
  19Q LOSS WILD-TYPE  356   56
                               clus
vv                              19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        26                356
  COLON MUCINOUS ADENOCARCINOMA                6                 56
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    21   0   3   3
  19Q LOSS WILD-TYPE 302   4  22  22
D75V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               21                302
  R1                0                  4
  R2                3                 22
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  1     0
  19Q LOSS WILD-TYPE                                0    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           3    12
  19Q LOSS WILD-TYPE                        56   200
D75V12, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       3                 56
  WHITE                                          12                200
[1] 4 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
  19Q LOSS MUTATED     0  16
  19Q LOSS WILD-TYPE   4 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   16
  19Q LOSS WILD-TYPE    4  253
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               16                253
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    36   6
  20P LOSS WILD-TYPE 299  95
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                394 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                 95 
$`20P LOSS MUTATED`
TCGA-AA-3867 TCGA-AA-3952 TCGA-G4-6298 TCGA-NH-A8F7 TCGA-A6-5666 TCGA-A6-5667 
       24.03         2.01        23.51        17.85        32.71        29.16 
TCGA-A6-6140 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3538 TCGA-AA-3553 TCGA-AA-3681 
       24.13        38.99         9.07        26.01        24.00         5.98 
TCGA-AA-3841 TCGA-AA-3855 TCGA-AA-3966 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01Z 
       36.95        32.05         2.01        34.03        42.02        37.02 
TCGA-AA-A03J TCGA-AZ-4308 TCGA-AZ-6606 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-5344 
       40.96       109.28        11.74        21.99         2.01        22.03 
TCGA-CM-5349 TCGA-CM-6168 TCGA-CM-6170 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6534 
       30.08        12.99        15.02        56.09        55.92        43.27 
TCGA-D5-6898 TCGA-D5-6923 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-F4-6809 TCGA-F4-6854 
        7.53        12.43        92.75        49.91        13.25         0.53 
TCGA-G4-6295 TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50V TCGA-RU-A8FL TCGA-SS-A7HO 
        8.35        36.00        26.43        19.33        38.70        60.13 

$`20P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       85.05        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       26.17        91.79        79.69        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        1.02        19.07         0.00        29.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 
       50.04        47.05        47.01        15.02        11.01        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 
       35.01         1.02        33.04         1.02        26.01        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       41.00        39.98        18.05        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6171 
       29.03        16.04        21.99        14.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 
       10.06        12.03        45.40        54.61        19.59        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        25.48        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20       130.65        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
       43.04        33.67        47.41        35.31       133.18        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       85.48        39.42        61.91        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       74.79        18.18        10.98        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        11.90        70.03 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.53               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            109.28             148.01 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            25.070             21.945 
[1] "0.5 - 109.3 (25.1)" "0.0 - 148.0 (21.9)"
[1] "hr=" "1.7"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20P LOSS MUTATED         7        0        2        12         1         1
  20P LOSS WILD-TYPE      67        1       27       120         9         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           3          0          9          3        4
  20P LOSS WILD-TYPE        17          8         50         38       41
                    vv
clus                 STAGE IVA STAGE IVB
  20P LOSS MUTATED           1         0
  20P LOSS WILD-TYPE        16         2
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   7                 67
  STAGE IA                  0                  1
  STAGE II                  2                 27
  STAGE IIA                12                120
  STAGE IIB                 1                  9
  STAGE IIC                 1                  0
  STAGE III                 3                 17
  STAGE IIIA                0                  8
  STAGE IIIB                9                 50
  STAGE IIIC                3                 38
  STAGE IV                  4                 41
  STAGE IVA                 1                 16
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED     0   7  30   6
  20P LOSS WILD-TYPE  11  70 275  49
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                0                 11
  T2                7                 70
  T3               30                275
  T4                6                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  20P LOSS MUTATED    23  13   7
  20P LOSS WILD-TYPE 239  92  75
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               23                239
  N1               13                 92
  N2                7                 75
[1] 3 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
  20P LOSS MUTATED    31   5
  20P LOSS WILD-TYPE 297  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     31    5
  20P LOSS WILD-TYPE  297   59
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               31                297
  1                5                 59
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    22  21
  20P LOSS WILD-TYPE 191 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     22   21
  20P LOSS WILD-TYPE  191  215
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               22                191
  MALE                 21                215
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    36   1
  20P LOSS WILD-TYPE 334   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     36    1
  20P LOSS WILD-TYPE  334    8
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                36                334
  YES                1                  8
[1] 2 2
[1] FALSE
D76V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    39   4
  20P LOSS WILD-TYPE 343  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     39    4
  20P LOSS WILD-TYPE  343   58
                               clus
vv                              20P LOSS MUTATED 20P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        39                343
  COLON MUCINOUS ADENOCARCINOMA                4                 58
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    32   0   2   2
  20P LOSS WILD-TYPE 291   4  23  23
D76V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               32                291
  R1                0                  4
  R2                2                 23
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     0
  20P LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           6    22
  20P LOSS WILD-TYPE                        53   190
D76V12, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       6                 53
  WHITE                                          22                190
[1] 4 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
  20P LOSS MUTATED     1  27
  20P LOSS WILD-TYPE   3 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   27
  20P LOSS WILD-TYPE    3  242
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               27                242
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     3   1
  20Q LOSS WILD-TYPE 332 100
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                432 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                100 
$`20Q LOSS MUTATED`
TCGA-AA-3952 TCGA-AA-3681 TCGA-CM-6168 TCGA-NH-A50V 
        2.01         5.98        12.99        19.33 

$`20Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99        24.00        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.36        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       74.79        18.18        10.98        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        38.70        60.13        11.90        70.03 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.01               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             19.33             148.01 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             9.485             22.090 
[1] "2.0 - 19.3 (9.5)"   "0.0 - 148.0 (22.1)"
[1] "hr=" "2.6"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20Q LOSS MUTATED         0        0        0         1         0         0
  20Q LOSS WILD-TYPE      74        1       29       131        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           1          0          1          1        0
  20Q LOSS WILD-TYPE        19          8         58         40       45
                    vv
clus                 STAGE IVA STAGE IVB
  20Q LOSS MUTATED           0         0
  20Q LOSS WILD-TYPE        17         2
D77V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                 74
  STAGE IA                  0                  1
  STAGE II                  0                 29
  STAGE IIA                 1                131
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 19
  STAGE IIIA                0                  8
  STAGE IIIB                1                 58
  STAGE IIIC                1                 40
  STAGE IV                  0                 45
  STAGE IVA                 0                 17
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     0   0   4   0
  20Q LOSS WILD-TYPE  11  77 301  55
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                0                 11
  T2                0                 77
  T3                4                301
  T4                0                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  20Q LOSS MUTATED     1   1   2
  20Q LOSS WILD-TYPE 261 104  80
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                1                261
  N1                1                104
  N2                2                 80
[1] 3 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
  20Q LOSS MUTATED     4   0
  20Q LOSS WILD-TYPE 324  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    0
  20Q LOSS WILD-TYPE  324   64
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                4                324
  1                0                 64
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   2
  20Q LOSS WILD-TYPE 211 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    2
  20Q LOSS WILD-TYPE  211  234
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                211
  MALE                  2                234
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   0
  20Q LOSS WILD-TYPE 367   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE  367    9
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 3                367
  YES                0                  9
[1] 2 2
[1] FALSE
D77V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4   0
  20Q LOSS WILD-TYPE 378  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    0
  20Q LOSS WILD-TYPE  378   62
                               clus
vv                              20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         4                378
  COLON MUCINOUS ADENOCARCINOMA                0                 62
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     4   0   0   0
  20Q LOSS WILD-TYPE 319   4  25  25
D77V10, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                4                319
  R1                0                  4
  R2                0                 25
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     0
  20Q LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           2     0
  20Q LOSS WILD-TYPE                        57   212
D77V12, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                281 
        TCGA-A6-2677         TCGA-A6-2681         TCGA-A6-2682 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-4105         TCGA-A6-6649         TCGA-AD-6548 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6895         TCGA-AD-6964 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AZ-4313         TCGA-AZ-4681         TCGA-AZ-6601 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-5912         TCGA-DM-A285 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G4-6294         TCGA-G4-6298         TCGA-G4-6310 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G4-6314         TCGA-G4-6321         TCGA-G4-6586 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-NH-A8F7         TCGA-3L-AA1B         TCGA-4N-A93T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-4T-AA8H         TCGA-5M-AAT4         TCGA-5M-AAT6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-5M-AATE         TCGA-A6-2671         TCGA-A6-2672 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2675         TCGA-A6-2676 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-2684         TCGA-A6-2685 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-2686         TCGA-A6-3807         TCGA-A6-3809 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-A6-5656 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-5657         TCGA-A6-5659         TCGA-A6-5660 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-5661         TCGA-A6-5662         TCGA-A6-5664 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-5665         TCGA-A6-5666         TCGA-A6-5667 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6140 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-6141         TCGA-A6-6142         TCGA-A6-6648 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-6650         TCGA-A6-6651         TCGA-A6-6652 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-6653         TCGA-A6-6654         TCGA-A6-6780 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-6781         TCGA-A6-6782         TCGA-A6-A565 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-A566         TCGA-A6-A567         TCGA-A6-A56B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A6-A5ZU         TCGA-AD-5900         TCGA-AD-6889 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6899         TCGA-AD-6901 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6965         TCGA-AD-A5EJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AD-A5EK         TCGA-AM-5820         TCGA-AM-5821 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AY-A54L 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AY-A69D         TCGA-AY-A71X         TCGA-AY-A8YK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AZ-4308         TCGA-AZ-4315         TCGA-AZ-4323 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AZ-4614         TCGA-AZ-4615         TCGA-AZ-4616 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-4684         TCGA-AZ-5403 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6603         TCGA-AZ-6605 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-CA-5254 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5256         TCGA-CA-5796 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CK-4951         TCGA-CK-4952         TCGA-CK-5913 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4748 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-4750         TCGA-CM-4751         TCGA-CM-4752 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6169 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6530         TCGA-D5-6531 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DM-A280         TCGA-DM-A282         TCGA-DM-A288 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DM-A28A         TCGA-DM-A28C         TCGA-DM-A28E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DM-A28F         TCGA-DM-A28G         TCGA-DM-A28H 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DM-A28K         TCGA-DM-A28M         TCGA-F4-6459 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6461         TCGA-F4-6463 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F4-6569         TCGA-F4-6570         TCGA-F4-6703 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F4-6704         TCGA-F4-6805         TCGA-F4-6806 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F4-6807         TCGA-F4-6808         TCGA-F4-6809 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F4-6854         TCGA-F4-6855         TCGA-F4-6856 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G4-6293         TCGA-G4-6295         TCGA-G4-6297 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6302         TCGA-G4-6303 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G4-6304         TCGA-G4-6306         TCGA-G4-6307 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G4-6309         TCGA-G4-6311         TCGA-G4-6315 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G4-6317         TCGA-G4-6320         TCGA-G4-6322 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6626         TCGA-G4-6627 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-NH-A50T         TCGA-NH-A50U         TCGA-NH-A5IV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-NH-A6GA         TCGA-NH-A6GB         TCGA-NH-A6GC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-NH-A8F8         TCGA-QG-A5YV         TCGA-QG-A5YW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QG-A5YX         TCGA-QG-A5Z1         TCGA-QG-A5Z2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-QL-A97D         TCGA-RU-A8FL         TCGA-SS-A7HO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-T9-A92H         TCGA-WS-AB45 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V13, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   2
  20Q LOSS WILD-TYPE   4 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    2
  20Q LOSS WILD-TYPE    4  267
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                2                267
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    91  26
  21Q LOSS WILD-TYPE 244  75
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               117                319 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                26                 75 
$`21Q LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3560 TCGA-AA-3688 TCGA-AA-3692 
       14.53        19.07        34.03        19.99        19.00        36.00 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-A00L TCGA-AA-A00Z TCGA-CK-5912 TCGA-G4-6314 
       14.93        24.03        38.04        21.99        49.08        35.93 
TCGA-G4-6625 TCGA-NH-A8F7 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
       91.79        17.85         1.61        39.45        43.76        43.76 
TCGA-A6-2684 TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6650 TCGA-A6-6651 
       37.05        30.44        22.06        29.16        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       24.39        23.87        20.28        61.84         9.63         5.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3538 TCGA-AA-3660 TCGA-AA-3685 
        6.97        38.99         9.07        26.01        78.08        37.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3866 
       10.06        38.99        37.02        10.06         0.99        17.03 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 
       18.05        24.00        20.98         2.01        21.99         7.96 
TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       13.94        27.02        42.02        15.02        10.98        32.02 
TCGA-AA-A01K TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 
       31.00        51.98        39.98        41.00        24.53        22.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A69D 
       26.47        16.44        14.50        16.31         0.20        17.85 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        5.13        65.00        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5914 TCGA-CM-4744 
       12.69        12.46        12.59        12.20        21.99        20.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
        8.02        27.02        13.02        22.03        22.98        32.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6677 
        5.03        15.02        14.04        29.03        15.02        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6929 TCGA-DM-A1D6 
       11.01        45.40        17.75        25.48        13.41        49.91 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6703 
      140.38         7.50       131.51        26.47        31.96        47.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
        1.55        41.42        43.04        33.67         0.53        47.41 
TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A50T 
        8.35        61.91        36.00        26.43        46.75        18.18 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-SS-A7HO 
        9.93        42.77        60.13 

$`21Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 
       13.02        24.03        37.05        36.03         8.05         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       85.05        19.04        19.04        31.07        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01         1.94         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-3L-AA1B 
       63.62        22.09        35.80        26.17        79.69        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        4.80        12.66         9.53        46.65        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       42.28        44.91        35.11        16.57        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 
       22.52        24.13         8.38        25.08        25.18        24.69 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3489 
       20.12        19.66        16.24        24.92        56.25         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        3.02         1.02        37.05        35.01        63.98         1.02 
TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        1.02        19.07         0.00        29.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       17.98        15.95        36.95         0.00        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 
       27.02        31.00         2.01        33.01        26.01        34.03 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 
       16.08        13.05        34.06        25.02        27.02        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
        4.01         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02H 
       33.04         1.02        26.01        37.02         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 
       12.16        83.24         5.79        27.42         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       11.74        12.36        12.39        12.59        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 
       37.02        25.02        26.04        29.06        30.08        15.02 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       13.05        11.08        10.06        12.03        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 
       56.09        55.92        20.19        20.42        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       13.32        12.59        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       14.04        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
        6.18        34.42        13.25        35.31       133.18        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U 
       85.48        39.42        26.04        13.78        74.79        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33        19.33        15.65        12.79        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       32.98         8.42        31.30        21.90        38.70        11.90 
TCGA-WS-AB45 
       70.03 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               0.2                0.0 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            140.38             148.01 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             22.03              22.09 
[1] "0.2 - 140.4 (22.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  21Q LOSS MUTATED        17        0        7        34         2         0
  21Q LOSS WILD-TYPE      57        1       22        98         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           4          3         13         17       18
  21Q LOSS WILD-TYPE        16          5         46         24       27
                    vv
clus                 STAGE IVA STAGE IVB
  21Q LOSS MUTATED           4         0
  21Q LOSS WILD-TYPE        13         2
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  17                 57
  STAGE IA                  0                  1
  STAGE II                  7                 22
  STAGE IIA                34                 98
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 4                 16
  STAGE IIIA                3                  5
  STAGE IIIB               13                 46
  STAGE IIIC               17                 24
  STAGE IV                 18                 27
  STAGE IVA                 4                 13
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q LOSS MUTATED     5  18  85  15
  21Q LOSS WILD-TYPE   6  59 220  40
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                5                  6
  T2               18                 59
  T3               85                220
  T4               15                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  21Q LOSS MUTATED    63  28  32
  21Q LOSS WILD-TYPE 199  77  50
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               63                199
  N1               28                 77
  N2               32                 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"
D78V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    82  22
  21Q LOSS WILD-TYPE 246  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     82   22
  21Q LOSS WILD-TYPE  246   42
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               82                246
  1               22                 42
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    59  64
  21Q LOSS WILD-TYPE 154 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     59   64
  21Q LOSS WILD-TYPE  154  172
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               59                154
  MALE                 64                172
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   103   3
  21Q LOSS WILD-TYPE 267   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    103    3
  21Q LOSS WILD-TYPE  267    6
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO               103                267
  YES                3                  6
[1] 2 2
[1] FALSE
D78V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   115   8
  21Q LOSS WILD-TYPE 267  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    115    8
  21Q LOSS WILD-TYPE  267   54
                               clus
vv                              21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       115                267
  COLON MUCINOUS ADENOCARCINOMA                8                 54
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED    85   2   8   6
  21Q LOSS WILD-TYPE 238   2  17  19
D78V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               85                238
  R1                2                  2
  R2                8                 17
  RX                6                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     4
  21Q LOSS WILD-TYPE                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          16    59
  21Q LOSS WILD-TYPE                        43   153
D78V12, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                      16                 43
  WHITE                                          59                153
[1] 4 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
  21Q LOSS MUTATED     3  73
  21Q LOSS WILD-TYPE   1 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3   73
  21Q LOSS WILD-TYPE    1  196
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  1
  NOT HISPANIC OR LATINO               73                196
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   104  37
  22Q LOSS WILD-TYPE 231  64
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               141                295 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                37                 64 
$`22Q LOSS MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3552 
       45.60        13.94        14.53        24.03        37.05        13.02 
TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 
       19.99         6.05        85.05        31.07        24.03        12.99 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
        2.01        50.99        26.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6625 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       63.62        91.79         4.80         1.61        39.45        43.76 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       42.28        44.91        35.11        16.57        34.65        36.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6650 
       31.63        30.44        29.19        23.61        22.52        20.61 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3511 
       21.76        23.87        61.84        56.25         9.63         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
       38.99         9.07        29.00        26.01        12.99        33.99 
TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 
       21.01        13.94         2.01        50.04        37.05        10.06 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        36.95        37.02        17.03        10.06        33.07 
TCGA-AA-3855 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3966 
       32.05        17.03        27.02        18.05         2.01         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O 
       21.99        13.05         7.96        13.94        34.03        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X 
       42.02        17.03        14.99        15.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 
       37.02        39.98        41.00        40.96         5.79        22.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A69D 
       26.47        16.44        14.50        16.31        33.01        17.85 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        1.41         5.65         5.13        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 
        3.19        12.36        12.20        14.30         2.01        25.02 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6170 
        8.02        29.06        30.08         5.03        15.02        15.02 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 
       11.08        11.01        45.40        56.09        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6929 
       43.27        15.12        17.85        12.49         7.53        13.41 
TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 
       11.38        12.59       140.38       131.51        26.47        31.96 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 
        1.55        43.04        13.25         8.35        82.39        61.91 
TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       36.00        46.75        18.18        10.98        19.33         9.93 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D 
       42.77        29.46        21.90 

$`22Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3524 
       24.33        24.16         1.02        58.03        13.02        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 
        8.05        19.07        34.03         0.99        17.95        23.01 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       14.93        29.98        24.00        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 
       75.95       106.75       100.01        28.21        23.51        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B 
       22.09        35.80        26.17        79.69        17.85        15.62 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       12.66         9.53        46.65        43.76        43.43        42.90 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        37.02        32.75        32.45        32.91 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.08        25.18        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3488 
       20.12        19.66        20.28        16.24        24.92         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3544 
        1.02         1.02        19.07         0.00        29.00        14.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        29.95        20.98        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02        14.01        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.98         5.03        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
        1.02        17.98        15.95         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 
       36.03         0.99        31.07        53.00        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 
       33.01        26.01        20.98        34.03        16.08        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       25.02        27.02        27.02        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 
       18.05        18.05         4.01         0.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02E 
        1.02        35.01         1.02         1.02        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 
       12.16        83.24        24.53        27.42         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95         0.20        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4682 
       19.33        18.84       109.28        58.39        32.94        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 
       65.00        62.79        88.21        49.41         6.77        11.74 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       12.69        12.46        12.39        12.59        12.59        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
       20.02        37.02        26.04        27.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       22.98        32.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       11.08        10.06        12.03        54.61        19.59        55.92 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       20.42        17.75        18.25         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50        44.32       135.65         7.76       139.17        14.04 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       47.87        34.42        41.42        33.67         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31       133.18        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 
       44.68        55.04        85.48        39.42        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       13.78        74.79        19.33        15.65        12.79        16.80 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        38.70        60.13        11.90 
TCGA-WS-AB45 
       70.03 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              1.41               0.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            140.38             148.01 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             21.90              22.09 
[1] "1.4 - 140.4 (21.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  22Q LOSS MUTATED        17        0        8        33         1         0
  22Q LOSS WILD-TYPE      57        1       21        99         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           5          6         16         21       24
  22Q LOSS WILD-TYPE        15          2         43         20       21
                    vv
clus                 STAGE IVA STAGE IVB
  22Q LOSS MUTATED           8         0
  22Q LOSS WILD-TYPE         9         2
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  17                 57
  STAGE IA                  0                  1
  STAGE II                  8                 21
  STAGE IIA                33                 99
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 5                 15
  STAGE IIIA                6                  2
  STAGE IIIB               16                 43
  STAGE IIIC               21                 20
  STAGE IV                 24                 21
  STAGE IVA                 8                  9
  STAGE IVB                 0                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED     3  22  97  22
  22Q LOSS WILD-TYPE   8  55 208  33
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                3                  8
  T2               22                 55
  T3               97                208
  T4               22                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  22Q LOSS MUTATED    64  43  37
  22Q LOSS WILD-TYPE 198  62  45
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               64                198
  N1               43                 62
  N2               37                 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"
D79V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    94  32
  22Q LOSS WILD-TYPE 234  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     94   32
  22Q LOSS WILD-TYPE  234   32
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               94                234
  1               32                 32
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    67  77
  22Q LOSS WILD-TYPE 146 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     67   77
  22Q LOSS WILD-TYPE  146  159
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               67                146
  MALE                 77                159
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   129   3
  22Q LOSS WILD-TYPE 241   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    129    3
  22Q LOSS WILD-TYPE  241    6
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               129                241
  YES                3                  6
[1] 2 2
[1] FALSE
D79V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   134  10
  22Q LOSS WILD-TYPE 248  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    134   10
  22Q LOSS WILD-TYPE  248   52
                               clus
vv                              22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       134                248
  COLON MUCINOUS ADENOCARCINOMA               10                 52
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    97   2  10  10
  22Q LOSS WILD-TYPE 226   2  15  15
D79V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               97                226
  R1                2                  2
  R2               10                 15
  RX               10                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     3
  22Q LOSS WILD-TYPE                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          22    63
  22Q LOSS WILD-TYPE                        37   149
D79V12, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                      22                 37
  WHITE                                          63                149
[1] 4 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
  22Q LOSS MUTATED     2  83
  22Q LOSS WILD-TYPE   2 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   83
  22Q LOSS WILD-TYPE    2  186
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               83                186
[1] 2 2
[1] FALSE

Clustering(80) Variable = XP LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    40  21
  XP LOSS WILD-TYPE 295  80
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               61               375 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               21                80 
$`XP LOSS MUTATED`
TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3952 TCGA-AA-3979 
       37.05        19.99        85.05        31.07         2.01        24.00 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-4N-A93T TCGA-A6-2678 TCGA-A6-2686 
      100.01        49.08         5.88         4.80        42.28        37.02 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3548 TCGA-AA-3679 
       61.84        56.25        38.99         9.07        33.99        15.02 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3941 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 
       10.06        38.99        24.00        21.99         7.96        13.94 
TCGA-AA-A00D TCGA-AA-A00R TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A02F 
       19.00         0.99        32.02        31.00        33.04        39.98 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6606 TCGA-AZ-6607 
       26.47        14.50        17.85         5.65        11.74         3.19 
TCGA-CA-5797 TCGA-CM-5348 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-D5-5537 
       12.59        22.98        15.02        11.01        13.05        45.40 
TCGA-D5-6923 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1HA 
       12.43        12.00        24.43        49.91       140.38       131.51 
TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6315 
       26.47        31.96        33.67         8.35        65.85        61.91 
TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-T9-A92H 
       26.04        10.98         9.93        15.65        16.80        11.90 
TCGA-WS-AB45 
       70.03 

$`XP LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 
       14.93        24.03        29.98        12.99        24.00        50.99 
TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       26.01        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6608 
       15.52        25.08        10.88        75.95       106.75         1.94 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H 
       26.17        91.79        79.69        17.85        15.62        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.43        42.90        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        32.75        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
       37.05        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.05        47.01        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
        2.01        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       27.02        38.04        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02        42.02        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       24.53         5.79        22.42        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.92        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        5.23        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       54.61        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.41        13.35        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        13.32        12.59         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        14.04        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       35.31       133.18        82.39        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        36.00        26.43 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        46.75        74.79        18.18        19.33        19.33 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       21.90        38.70        60.13 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.99              0.00 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           140.38            148.01 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            24.00             22.03 
[1] "1.0 - 140.4 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XP LOSS MUTATED         7        0        3        15         0         0
  XP LOSS WILD-TYPE      67        1       26       117        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           4          0          9         10       11
  XP LOSS WILD-TYPE        16          8         50         31       34
                   vv
clus                STAGE IVA STAGE IVB
  XP LOSS MUTATED           3         1
  XP LOSS WILD-TYPE        14         1
D80V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  7                67
  STAGE IA                 0                 1
  STAGE II                 3                26
  STAGE IIA               15               117
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                4                16
  STAGE IIIA               0                 8
  STAGE IIIB               9                50
  STAGE IIIC              10                31
  STAGE IV                11                34
  STAGE IVA                3                14
  STAGE IVB                1                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP LOSS MUTATED     1   6  45  11
  XP LOSS WILD-TYPE  10  71 260  44
D80V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               1                10
  T2               6                71
  T3              45               260
  T4              11                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  XP LOSS MUTATED    25  17  21
  XP LOSS WILD-TYPE 237  88  61
D80V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              25               237
  N1              17                88
  N2              21                61
[1] 3 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
  XP LOSS MUTATED    42  15
  XP LOSS WILD-TYPE 286  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     42   15
  XP LOSS WILD-TYPE  286   49
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              42               286
  1              15                49
[1] 2 2
[1] FALSE
D80V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    24  39
  XP LOSS WILD-TYPE 189 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     24   39
  XP LOSS WILD-TYPE  189  197
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              24               189
  MALE                39               197
[1] 2 2
[1] FALSE
D80V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    53   0
  XP LOSS WILD-TYPE 317   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     53    0
  XP LOSS WILD-TYPE  317    9
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               53               317
  YES               0                 9
[1] 2 2
[1] FALSE
D80V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    57   6
  XP LOSS WILD-TYPE 325  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     57    6
  XP LOSS WILD-TYPE  325   56
                               clus
vv                              XP LOSS MUTATED XP LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       57               325
  COLON MUCINOUS ADENOCARCINOMA               6                56
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    44   1   4   3
  XP LOSS WILD-TYPE 279   3  21  22
D80V10, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              44               279
  R1               1                 3
  R2               4                21
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0     1
  XP LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                          11    27
  XP LOSS WILD-TYPE                        48   185
D80V12, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     11                48
  WHITE                                         27               185
[1] 4 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
  XP LOSS MUTATED     0  38
  XP LOSS WILD-TYPE   4 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0   38
  XP LOSS WILD-TYPE    4  231
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              38               231
[1] 2 2
[1] FALSE

Clustering(81) Variable = XQ LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    35  14
  XQ LOSS WILD-TYPE 300  87
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               49               387 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               14                87 
$`XQ LOSS MUTATED`
TCGA-AA-3522 TCGA-AA-3860 TCGA-AA-3952 TCGA-AA-3979 TCGA-CK-5912 TCGA-4N-A93T 
       37.05        31.07         2.01        24.00        49.08         4.80 
TCGA-A6-2678 TCGA-A6-A567 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3548 TCGA-AA-3679 
       42.28        61.84        38.99         9.07        33.99        15.02 
TCGA-AA-3837 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A00D 
       38.99        24.00         2.01        21.99         7.96        19.00 
TCGA-AA-A00R TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02F TCGA-AD-6965 TCGA-AU-3779 
        0.99        32.02        31.00        39.98        26.47        14.50 
TCGA-AY-5543 TCGA-AY-A69D TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CK-6748 
       33.01        17.85        11.74         3.19        12.59         2.01 
TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-5537 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D6 
       15.02        11.01        45.40        12.00        24.43        49.91 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6303 
      140.38       131.51        26.47        33.67         8.35        65.85 
TCGA-G4-6315 TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-SS-A7HO 
       61.91        26.04        10.98         9.93        16.80        60.13 
TCGA-T9-A92H 
       11.90 

$`XQ LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       24.00        50.99        26.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01         1.94         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       79.69        17.85        15.62        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
       37.05        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.05        47.01        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       34.03        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       16.44         0.46         0.92        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
        0.20        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       12.10        29.56         5.23        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        14.04        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       13.32        12.59         7.50        44.32       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
      133.18        82.39        74.56        67.30        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 
       55.04        85.48        39.42        36.00        26.43        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       46.75        74.79        18.18        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       21.90        38.70        70.03 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.99              0.00 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           140.38            148.01 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            24.00             22.03 
[1] "1.0 - 140.4 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XQ LOSS MUTATED         6        0        1        13         1         0
  XQ LOSS WILD-TYPE      68        1       28       119         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           1          0          6          8       11
  XQ LOSS WILD-TYPE        19          8         53         33       34
                   vv
clus                STAGE IVA STAGE IVB
  XQ LOSS MUTATED           3         0
  XQ LOSS WILD-TYPE        14         2
D81V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  6                68
  STAGE IA                 0                 1
  STAGE II                 1                28
  STAGE IIA               13               119
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                19
  STAGE IIIA               0                 8
  STAGE IIIB               6                53
  STAGE IIIC               8                33
  STAGE IV                11                34
  STAGE IVA                3                14
  STAGE IVB                0                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED     1   5  33  11
  XQ LOSS WILD-TYPE  10  72 272  44
D81V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               1                10
  T2               5                72
  T3              33               272
  T4              11                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  XQ LOSS MUTATED    21  14  15
  XQ LOSS WILD-TYPE 241  91  67
D81V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              21               241
  N1              14                91
  N2              15                67
[1] 3 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
  XQ LOSS MUTATED    32  14
  XQ LOSS WILD-TYPE 296  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     32   14
  XQ LOSS WILD-TYPE  296   50
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              32               296
  1              14                50
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    20  30
  XQ LOSS WILD-TYPE 193 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     20   30
  XQ LOSS WILD-TYPE  193  206
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              20               193
  MALE                30               206
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    41   0
  XQ LOSS WILD-TYPE 329   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     41    0
  XQ LOSS WILD-TYPE  329    9
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               41               329
  YES               0                 9
[1] 2 2
[1] FALSE
D81V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    44   6
  XQ LOSS WILD-TYPE 338  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     44    6
  XQ LOSS WILD-TYPE  338   56
                               clus
vv                              XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       44               338
  COLON MUCINOUS ADENOCARCINOMA               6                56
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    32   1   4   3
  XQ LOSS WILD-TYPE 291   3  21  22
D81V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              32               291
  R1               1                 3
  R2               4                21
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     1
  XQ LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           9    21
  XQ LOSS WILD-TYPE                        50   191
D81V12, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      9                50
  WHITE                                         21               191
[1] 4 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
  XQ LOSS MUTATED     0  30
  XQ LOSS WILD-TYPE   4 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   30
  XQ LOSS WILD-TYPE    4  239
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              30               239
[1] 2 2
[1] FALSE
