[1] "ofn"        "-oTSTES-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/STES-TP/22507048/STES-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/22532763/transformed.cor.cli.txt"

nPatients in clinical file=628, in cluster file=625, common to both=625
[1]  82 625
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               84               541 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               84               541 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              170               455 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              170               455 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              137               488 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              137               488 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              113               512 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              113               512 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               85               540 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               85               540 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              170               455 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              170               455 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               37               588 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               37               588 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               30               595 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               30               595 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              179               446 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              179               446 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               64               561 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               64               561 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              118               507 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              118               507 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              100               525 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              100               525 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              308               317 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              308               317 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              257               368 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              257               368 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              248               377 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              248               377 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              337               288 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              337               288 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               78               547 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               78               547 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              109               516 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              109               516 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               136                489 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               136                489 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                98                527 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                98                527 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                98                527 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                98                527 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               102                523 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               102                523 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               149                476 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               149                476 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               116                509 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               116                509 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               197                428 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               197                428 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                76                549 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                76                549 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                67                558 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                67                558 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               100                525 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               100                525 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                86                539 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                86                539 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                61                564 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                61                564 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               108                517 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               108                517 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               135                490 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               135                490 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                79                546 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                79                546 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                83                542 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                83                542 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               119                506 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               119                506 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               349                276 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               349                276 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               395                230 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               395                230 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                39                586 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                39                586 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                63                562 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                63                562 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               75               550 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               75               550 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               93               532 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               93               532 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               97               528 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               97               528 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47               578 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47               578 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               36               589 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               36               589 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               49               576 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               49               576 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              187               438 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              187               438 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               92               533 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               92               533 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              274               351 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              274               351 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              256               369 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              256               369 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              110               515 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              110               515 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              195               430 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              195               430 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               93               532 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               93               532 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              112               513 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              112               513 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               33               592 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               33               592 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               50               575 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               50               575 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              156               469 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              156               469 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               59               566 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               59               566 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              249               376 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              249               376 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              173               452 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              173               452 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               118                507 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               118                507 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               118                507 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               118                507 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               117                508 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               117                508 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               122                503 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               122                503 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                98                527 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                98                527 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                87                538 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                87                538 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               103                522 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               103                522 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               157                468 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               157                468 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               149                476 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               149                476 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               154                471 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               154                471 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               167                458 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               167                458 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               237                388 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               237                388 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               102                523 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               102                523 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               187                438 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               187                438 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               257                368 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               257                368 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               182                443 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               182                443 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               142                483 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               142                483 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                583 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                583 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                617 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                617 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               287                338 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               287                338 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               218                407 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               218                407 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              123               502 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              123               502 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               98               527 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               98               527 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"              "VITAL_STATUS"               
 [3] "DAYS_TO_DEATH"               "DAYS_TO_LAST_FOLLOWUP"      
 [5] "PATHOLOGIC_STAGE"            "PATHOLOGY_T_STAGE"          
 [7] "PATHOLOGY_N_STAGE"           "PATHOLOGY_M_STAGE"          
 [9] "GENDER"                      "RADIATION_THERAPY"          
[11] "KARNOFSKY_PERFORMANCE_SCORE" "NUMBER_PACK_YEARS_SMOKED"   
[13] "RACE"                        "ETHNICITY"                  

Input Data has 14 rows and 625 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=215,	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=298,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'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 625 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "NUMBER_PACK_YEARS_SMOKED"    "RACE"                       
[11] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=56, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  54 136 283 124 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   55   136   283   124 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  54 136 283 124 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   55   136   283   124 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
207 187  98  96 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
207 187  98  96 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
207 187  98  96 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
207 187  98  96 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=46, 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    42  35
  1P GAIN WILD-TYPE 312 210
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               77               522 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               35               210 
$`1P GAIN MUTATED`
TCGA-L5-A88Y TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A93E 
        0.36        13.94        35.21        17.03         4.67        25.22 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       47.93        18.35         7.43         3.75         3.02         2.66 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       13.22        13.41        10.85        10.36         5.92        10.45 
TCGA-LN-A49X TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.62        13.38         0.13        12.03        12.85        12.26 
TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8EW 
       38.40        15.78        12.69         3.42        22.82         8.12 
TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-7717 
       25.08         2.10        19.73         9.67         6.18        18.15 
TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8588 
        3.45        29.42         7.36         5.39        25.18        12.79 
TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-CD-A48A TCGA-CG-4436 TCGA-D7-6521 
        8.22         0.72        13.51        12.43         7.99        18.54 
TCGA-D7-6820 TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-HJ-7597 TCGA-HU-8243 
       11.31        16.44        22.29         7.99        26.47         5.92 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-A6RI 
       25.81        11.77         8.98         6.58        12.95        18.38 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-KB-A6F7 TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MV 
        6.44         6.74        63.62         6.08        16.67       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PK 
      115.69         8.94        48.79        18.48        43.36        17.85 
TCGA-VQ-A8PZ TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A 
       73.41        42.54        11.24        18.41        38.93 

$`1P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       16.24         0.23        20.15         9.86        27.35        26.93 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       32.61        21.01         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.13        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       25.12         7.40        55.50        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.55         7.76         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       52.57        46.09        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
       13.38        13.15        15.35        12.59        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.33        13.18        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         2.30         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 
       41.23        14.37         3.42         1.32         2.66        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         4.08         9.34         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       39.78        15.32        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27        14.79        25.05         3.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        20.88        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        12.36        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68        24.20         3.25        22.75        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        0.10         6.51        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81         3.39        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
       19.53        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW 
        4.60         9.24        11.05         8.61         5.13        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        14.33        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
        2.66        43.66        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.13              0.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            122.3             122.1 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           12.790            14.285 
[1] "0.1 - 122.3 (12.8)" "0.0 - 122.1 (14.3)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         2        3        7        2        12        13
  1P GAIN WILD-TYPE       8       18       40       31        75        74
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           3          8         12          7        1
  1P GAIN WILD-TYPE        25         87         60         39       48
                   vv
clus                STAGE IVA
  1P GAIN MUTATED           2
  1P GAIN WILD-TYPE         2
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 3                18
  STAGE IB                 7                40
  STAGE II                 2                31
  STAGE IIA               12                75
  STAGE IIB               13                74
  STAGE III                3                25
  STAGE IIIA               8                87
  STAGE IIIB              12                60
  STAGE IIIC               7                39
  STAGE IV                 1                48
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1P GAIN MUTATED      12  19  38   9
  1P GAIN WILD-TYPE    43 117 245 115
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1              12                43
  T2                 19               117
  T3                 38               245
  T4                  9               115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P GAIN MUTATED    28  23  13  11
  1P GAIN WILD-TYPE 179 164  85  85
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              28               179
  N1              23               164
  N2              13                85
  N3              11                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"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    70   2
  1P GAIN WILD-TYPE 454  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     70    2
  1P GAIN WILD-TYPE  454   37
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              70               454
  1               2                37
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    18  66
  1P GAIN WILD-TYPE 167 374
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     18   66
  1P GAIN WILD-TYPE  167  374
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              18               167
  MALE                66               374
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    51  23
  1P GAIN WILD-TYPE 394  96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     51   23
  1P GAIN WILD-TYPE  394   96
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               51               394
  YES              23                96
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED      20                         5
  1P GAIN WILD-TYPE   114                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           0    54
  1P GAIN WILD-TYPE                                         1   338
D1V11, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                                  20               114
  BLACK OR AFRICAN AMERICAN                               5                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  54               338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2  58
  1P GAIN WILD-TYPE   9 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   58
  1P GAIN WILD-TYPE    9  346
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              58               346
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    90  72
  1Q GAIN WILD-TYPE 264 173
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              162               437 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               72               173 
$`1Q GAIN MUTATED`
TCGA-L5-A88Y TCGA-CG-4460 TCGA-VQ-A94U TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A3QL 
        0.36        21.99        26.93        13.94         8.94        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        0.85        20.12        18.64        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF 
       12.82         4.67        31.56        25.22         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88Z 
       32.61        47.93        18.35         4.90         7.43         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NL 
        3.75         3.02        55.50         2.66        12.92        13.22 
TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        5.49        13.41        10.85        10.36         5.92        10.45 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4MR 
       15.35        12.59        12.62        12.49        12.76        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
        4.47        12.33        12.00        13.18        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8W5 
       12.03        12.85        12.26        16.31        38.40        15.78 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EX 
       12.69        20.38         3.42        22.82         8.12        28.11 
TCGA-VR-AA4D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       46.19        15.91        18.21        25.08         2.10         1.32 
TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6705 
       19.73        11.01         4.08         9.67         6.18        25.61 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8360 
       18.15        28.73         3.45        29.42         2.20         6.18 
TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       14.04         7.36         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4J1 
        1.12        12.79        31.96         8.22         7.53         0.72 
TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8533 
       28.34        13.51        20.42        12.76        12.39        15.39 
TCGA-CD-8535 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CG-4436 TCGA-CG-4438 TCGA-D7-5578 
       12.82        11.61         6.58         7.99        54.08        12.66 
TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 
       20.91        18.54        17.19        10.26        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YU TCGA-D7-A6EX 
       11.31        12.33        24.72        19.50        16.44        11.31 
TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 
       22.29         0.62         7.99        72.23         3.48        14.07 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56         5.52        52.21        30.51        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
        5.92        24.39        28.96        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-A6RP TCGA-KB-A6F7 
        0.10         6.58        12.95         3.45         6.44        63.62 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N6 
       18.21         6.08        16.67       122.30       115.69         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       35.61        48.79         5.46        13.02        18.48        43.36 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91S 
        2.70        17.85        14.33        73.41        39.45        32.88 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A 
       66.81        21.04        42.54        11.24        18.41        38.93 

$`1Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH 
        0.23        20.15         9.86        27.35        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30        58.55         7.63         5.92        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS 
       32.45         7.69        33.27        20.78         2.63         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        9.30         0.53         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        24.03         6.28         3.16        30.25 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NI 
       29.00         7.13        15.48         2.60        25.12        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       16.47        13.55         7.76        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       52.57        46.09        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 
       13.38        13.15        13.25        12.46        12.59        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U7 
       22.39        12.85        15.52        11.54        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-M9-A5M8 
       10.52        12.23        12.03        12.33        13.18        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ 
        7.82         8.02         7.59         5.06         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB 
       53.95         9.30         2.89         2.30         7.00         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.43         1.55        18.31        33.70        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.05        11.24         9.17        41.23        14.37         3.42 
TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        2.66        58.03        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       30.90         4.08         9.34         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        32.78        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       15.32         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        0.56         2.66        19.96        15.58         7.40        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
        4.31         3.32        11.80        31.27        14.79        25.05 
TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        3.72        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       26.73        24.79        32.58         9.86        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       28.57        12.89         8.98        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52         0.46        20.65         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       11.21        12.10        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 
       12.30        12.59        11.64        12.07        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31        12.43        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        25.71        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8572 
       18.61        17.85        13.35        15.22        15.98        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 
        7.13        14.47        21.27        11.38        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       17.06        59.54         5.03         6.21        77.29        63.06 
TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       22.75        21.37        29.98         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        5.13        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8E3 
       16.87        19.04         5.79         0.92        13.25        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM 
       46.26        16.31        22.19         2.50        12.79         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       11.70        21.83        61.22        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P 
        2.01        55.43         4.54         6.58         5.72         2.66 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              0.1               0.0 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            122.3             122.1 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           12.985            14.470 
[1] "0.1 - 122.3 (13.0)" "0.0 - 122.1 (14.5)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         2        7       13        7        22        24
  1Q GAIN WILD-TYPE       8       14       34       26        65        63
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           8         25         20         13       10
  1Q GAIN WILD-TYPE        20         70         52         33       39
                   vv
clus                STAGE IVA
  1Q GAIN MUTATED           3
  1Q GAIN WILD-TYPE         1
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 7                14
  STAGE IB                13                34
  STAGE II                 7                26
  STAGE IIA               22                65
  STAGE IIB               24                63
  STAGE III                8                20
  STAGE IIIA              25                70
  STAGE IIIB              20                52
  STAGE IIIC              13                33
  STAGE IV                10                39
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1Q GAIN MUTATED      21  37  77  28
  1Q GAIN WILD-TYPE    34  99 206  96
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              21                34
  T2                 37                99
  T3                 77               206
  T4                 28                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED    56  48  28  26
  1Q GAIN WILD-TYPE 151 139  70  70
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              56               151
  N1              48               139
  N2              28                70
  N3              26                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   138  12
  1Q GAIN WILD-TYPE 386  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    138   12
  1Q GAIN WILD-TYPE  386   27
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             138               386
  1              12                27
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    40 130
  1Q GAIN WILD-TYPE 145 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     40  130
  1Q GAIN WILD-TYPE  145  310
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              40               145
  MALE               130               310
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   114  41
  1Q GAIN WILD-TYPE 331  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    114   41
  1Q GAIN WILD-TYPE  331   78
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              114               331
  YES              41                78
[1] 2 2
[1] FALSE
D2V9, continuous
D2V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED      43                        10
  1Q GAIN WILD-TYPE    91                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           0   105
  1Q GAIN WILD-TYPE                                         1   287
D2V11, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                                  43                91
  BLACK OR AFRICAN AMERICAN                              10                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 105               287
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2 118
  1Q GAIN WILD-TYPE   9 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2  118
  1Q GAIN WILD-TYPE    9  286
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO             118               286
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    79  52
  2P GAIN WILD-TYPE 275 193
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              131               468 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               52               193 
$`2P GAIN MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A88Y TCGA-CG-4460 TCGA-CG-5727 TCGA-MX-A663 
       15.68         4.31         0.36        21.99        79.07         9.86 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6FA 
       13.94         8.94        18.64        23.41         4.67        44.75 
TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       25.22        26.33        32.61        47.93        18.35         3.32 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ 
        3.16         7.13         2.60        52.57        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
        5.92        13.38        13.15        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.76        12.59        12.85        12.33        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN 
       12.00        12.33        13.18        12.85        12.26         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP 
       53.95        12.69        20.38         3.42        15.35        27.09 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7B 
       18.31         8.12        28.11        33.70        46.19        11.24 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6566 
       18.21        25.08        11.01         6.61        17.29        32.78 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8077 TCGA-BR-8080 
        9.21        35.24        33.63        18.15         0.69         9.60 
TCGA-BR-8295 TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-A4CS 
        2.20        13.08         5.39         9.21        20.22         1.48 
TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5800 TCGA-CD-5801 
       12.89        13.51        20.65        20.42        13.15        13.18 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 TCGA-D7-6521 
       13.35        12.76        12.00        36.00        12.03        18.54 
TCGA-D7-6815 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-FP-A9TM 
       15.98        18.21        16.44        11.24        15.65         6.21 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GF 
       28.96         0.76        24.30        24.26        22.75        25.81 
TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD 
        8.98         2.10        12.95        23.84        23.80        33.40 
TCGA-IN-7808 TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A93H 
        3.45         6.74        12.59        10.62         5.56        37.64 
TCGA-R5-A7ZE TCGA-RD-A8N6 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PE TCGA-VQ-A8PH 
       18.21         8.94        43.36        21.73        22.19        12.79 
TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6A 
       17.85        20.81         1.71        66.81        43.66        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       32.94        16.14        27.55        17.26         0.79 

$`2P GAIN WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       47.05        22.98        16.24         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       26.93        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        5.92        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86        14.50        12.16       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       41.52        47.38        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OP 
        6.28         3.16        30.25         0.30        21.01         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        1.38        58.59         4.90        29.00         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        83.24        46.09 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        12.33        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        13.25        12.62        22.39        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.22         4.47        10.52        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6Y2 
       13.38         0.13        12.03        33.11         7.82         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
       15.78         2.89         2.30         7.00         5.29        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        22.82        12.43         1.55 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 
       18.18        52.27        18.05         9.17        15.91        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       36.16        35.84        39.78        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96        15.58         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        25.18         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08        34.98        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52         0.46         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 
       13.41        13.02        11.21        12.10        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       26.43        11.31        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH 
       21.07         5.59        22.68        24.20         3.25        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        0.26        29.00        21.17        14.07        15.68        36.36 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.44         6.51        11.70        15.75        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        18.48        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       30.97        34.29        46.26        16.31         2.50         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        32.88        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       18.41        28.41        17.13        54.12        26.04        12.43 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.36              0.00 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            79.07            122.30 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            13.18             14.07 
[1] "0.4 - 79.1 (13.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         1        8        7        8        19        25
  2P GAIN WILD-TYPE       9       13       40       25        68        62
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           6         12         14         11        8
  2P GAIN WILD-TYPE        22         83         58         35       41
                   vv
clus                STAGE IVA
  2P GAIN MUTATED           1
  2P GAIN WILD-TYPE         3
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 8                13
  STAGE IB                 7                40
  STAGE II                 8                25
  STAGE IIA               19                68
  STAGE IIB               25                62
  STAGE III                6                22
  STAGE IIIA              12                83
  STAGE IIIB              14                58
  STAGE IIIC              11                35
  STAGE IV                 8                41
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2P GAIN MUTATED      18  25  63  19
  2P GAIN WILD-TYPE    37 111 220 105
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              18                37
  T2                 25               111
  T3                 63               220
  T4                 19               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P GAIN MUTATED    48  36  18  22
  2P GAIN WILD-TYPE 159 151  80  74
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              48               159
  N1              36               151
  N2              18                80
  N3              22                74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   106   7
  2P GAIN WILD-TYPE 418  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    106    7
  2P GAIN WILD-TYPE  418   32
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0             106               418
  1               7                32
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    37 100
  2P GAIN WILD-TYPE 148 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     37  100
  2P GAIN WILD-TYPE  148  340
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              37               148
  MALE               100               340
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   100  25
  2P GAIN WILD-TYPE 345  94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    100   25
  2P GAIN WILD-TYPE  345   94
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO              100               345
  YES              25                94
[1] 2 2
[1] FALSE
D3V9, continuous
D3V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED      41                         5
  2P GAIN WILD-TYPE    93                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           0    78
  2P GAIN WILD-TYPE                                         1   314
D3V11, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                                  41                93
  BLACK OR AFRICAN AMERICAN                               5                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  78               314
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  91
  2P GAIN WILD-TYPE   9 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   91
  2P GAIN WILD-TYPE    9  313
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              91               313
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    63  45
  2Q GAIN WILD-TYPE 291 200
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              108               491 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               45               200 
$`2Q GAIN MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A88Y TCGA-CG-4460 TCGA-CG-5727 TCGA-MX-A663 
       15.68         4.31         0.36        21.99        79.07         9.86 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A5S3 TCGA-JY-A6FA TCGA-JY-A93E TCGA-L5-A4OF 
       13.94         8.94        23.41        44.75        25.22        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A8NE 
       32.61        47.93         3.32         7.13         2.60        55.50 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A4A1 TCGA-LN-A4A2 
       52.57        10.85         5.92        13.38        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8HZ 
       12.59        12.85        12.33        25.25        12.00        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18        12.85        12.26         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG 
        5.06        16.31        38.40         6.35        53.95        12.69 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-AA4D 
        3.42        16.44        27.09        18.31        28.11        46.19 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-B7-A5TJ TCGA-BR-6456 TCGA-BR-6566 TCGA-BR-7197 
       18.21        25.08        11.01        17.29        32.78         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 
       35.24        33.63        18.15         0.69         9.60         2.20 
TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 
       13.08         5.39         9.21         1.48        12.89         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-A48C TCGA-CG-5718 
       13.51        20.42        13.18        12.76        11.61        36.00 
TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-EQ-8122 
       12.03        18.54        15.98        16.44        11.24         7.99 
TCGA-F1-6875 TCGA-FP-A9TM TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF 
       72.23         6.21         0.76        24.30        24.26        25.81 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-A6RR 
        2.10        12.95        23.84        23.80         3.45         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A8N6 TCGA-VQ-A8E2 
       12.59        10.62         5.56        37.64         8.94        43.36 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D 
       22.19        12.79        17.85        20.81         1.71        66.81 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       38.93        32.94        16.14        27.55        17.26         0.79 

$`2Q GAIN WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       47.05        22.98        16.24         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       26.93        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        5.92        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        3.88         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.43        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       13.41        83.24        46.09        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 
       13.25        12.62        12.46        12.76        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       11.54        12.33        13.22         4.47        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 
       12.03        13.18        13.38         0.13        12.03        33.11 
TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.04         9.30        15.78         2.89         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.38         5.29        15.35         9.27         8.98        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       22.82        12.43         1.55         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 
       52.27        18.05        11.24         9.17        15.91        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       21.90        36.16        35.84        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44        29.59        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96        15.58         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       25.05         3.72        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
       28.34        32.52         0.46        20.65         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       16.14         5.13        13.41        13.02        13.15        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       11.21        12.10        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 
        4.34        19.96         7.13         0.62        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7132 
       59.54         5.03        13.58         0.56         5.52        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        5.59        22.68        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       20.25         0.26        29.00        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
       13.35        19.53         6.44         6.51        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 
       48.79         5.46        13.25        13.02        18.48        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.50         2.70         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       32.88        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       28.41        17.13        54.12        26.04        12.43 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.36              0.00 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            79.07            122.30 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            13.13             14.07 
[1] "0.4 - 79.1 (13.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         1        6        6        6        15        23
  2Q GAIN WILD-TYPE       9       15       41       27        72        64
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           4          7         13          8        6
  2Q GAIN WILD-TYPE        24         88         59         38       43
                   vv
clus                STAGE IVA
  2Q GAIN MUTATED           1
  2Q GAIN WILD-TYPE         3
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 6                15
  STAGE IB                 6                41
  STAGE II                 6                27
  STAGE IIA               15                72
  STAGE IIB               23                64
  STAGE III                4                24
  STAGE IIIA               7                88
  STAGE IIIB              13                59
  STAGE IIIC               8                38
  STAGE IV                 6                43
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2Q GAIN MUTATED      15  23  49  15
  2Q GAIN WILD-TYPE    40 113 234 109
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              15                40
  T2                 23               113
  T3                 49               234
  T4                 15               109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q GAIN MUTATED    38  31  13  18
  2Q GAIN WILD-TYPE 169 156  85  78
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              38               169
  N1              31               156
  N2              13                85
  N3              18                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    87   6
  2Q GAIN WILD-TYPE 437  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     87    6
  2Q GAIN WILD-TYPE  437   33
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              87               437
  1               6                33
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    31  82
  2Q GAIN WILD-TYPE 154 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     31   82
  2Q GAIN WILD-TYPE  154  358
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              31               154
  MALE                82               358
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    84  19
  2Q GAIN WILD-TYPE 361 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     84   19
  2Q GAIN WILD-TYPE  361  100
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               84               361
  YES              19               100
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED      29                         5
  2Q GAIN WILD-TYPE   105                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           0    68
  2Q GAIN WILD-TYPE                                         1   324
D4V11, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                                  29               105
  BLACK OR AFRICAN AMERICAN                               5                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  68               324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  75
  2Q GAIN WILD-TYPE   9 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   75
  2Q GAIN WILD-TYPE    9  329
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              75               329
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    48  34
  3P GAIN WILD-TYPE 306 211
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               82               517 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               34               211 
$`3P GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-5727 TCGA-2H-A9GH 
        4.31        27.12         5.16        47.05        79.07        31.27 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OM 
       16.24         7.69        23.18        25.22         0.30        47.93 
TCGA-L5-A4OR TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NV TCGA-L7-A56G 
        3.16         3.75        55.50        16.47        52.57        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A4A1 TCGA-R6-A6KZ 
       10.36        10.45        13.41        13.38        12.59         5.06 
TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EX 
       53.95        12.69         9.27        22.82        12.43        28.11 
TCGA-VR-AA7B TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-BR-4255 TCGA-BR-4257 
       11.24        14.37         1.32        19.73         4.08         9.67 
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 
        6.18        34.68         9.17        30.90        21.90        15.32 
TCGA-BR-7901 TCGA-BR-8296 TCGA-BR-8373 TCGA-BR-A4J7 TCGA-CD-5799 TCGA-CD-5801 
        3.45        15.58        14.79        32.52        13.02        13.18 
TCGA-CD-8528 TCGA-CG-4477 TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-A4YU 
       12.33        30.97        12.03        18.54        15.98        16.44 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-F1-A448 TCGA-FP-7998 TCGA-HU-A4G9 TCGA-HU-A4GF 
       11.24        22.29        21.27        22.29        24.20        25.81 
TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4HD 
        8.98         2.10        12.95        29.00        23.80        33.40 
TCGA-R5-A7ZR TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8P5 TCGA-VQ-A8PK 
        6.08       115.69        35.61        48.79         7.73        17.85 
TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Y 
       23.41        13.35        64.57        73.41        21.83         9.73 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A94O TCGA-VQ-AA6F 
        9.04         2.01        21.04        54.12 

$`3P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV 
        4.70        19.99        22.82         0.36        35.97        20.02 
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       27.35        26.93        25.78        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
        5.92        13.94         8.94         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
       15.48         2.60        25.12         7.40         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K 
       21.37         8.71        13.41        83.24        46.09         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.66        12.43        12.33        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59        16.31         7.04        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         8.98        25.81        27.09 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        18.05         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 
       41.23         3.42         2.10         2.66        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.34         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       39.78        18.15        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.41        13.15        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        12.00         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       30.51        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        5.59        24.26        22.68         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        0.26        23.84        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52        74.53         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79         0.92         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       43.36        21.73        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY 
        2.70         1.87         9.27        15.65        29.59        14.33 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       39.45        11.70        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A924 
        1.71        42.64        60.85         9.50        55.56        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        66.81         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              0.3               0.0 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           115.69            122.30 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            15.78             13.68 
[1] "0.3 - 115.7 (15.8)" "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         0        4        5        4         8        13
  3P GAIN WILD-TYPE      10       17       42       29        79        74
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           6         11          9          9        6
  3P GAIN WILD-TYPE        22         84         63         37       43
                   vv
clus                STAGE IVA
  3P GAIN MUTATED           2
  3P GAIN WILD-TYPE         2
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 4                17
  STAGE IB                 5                42
  STAGE II                 4                29
  STAGE IIA                8                79
  STAGE IIB               13                74
  STAGE III                6                22
  STAGE IIIA              11                84
  STAGE IIIB               9                63
  STAGE IIIC               9                37
  STAGE IV                 6                43
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3P GAIN MUTATED       8  14  41  16
  3P GAIN WILD-TYPE    47 122 242 108
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1               8                47
  T2                 14               122
  T3                 41               242
  T4                 16               108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P GAIN MUTATED    23  27  11  16
  3P GAIN WILD-TYPE 184 160  87  80
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              23               184
  N1              27               160
  N2              11                87
  N3              16                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    69   5
  3P GAIN WILD-TYPE 455  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     69    5
  3P GAIN WILD-TYPE  455   34
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              69               455
  1               5                34
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    23  62
  3P GAIN WILD-TYPE 162 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     23   62
  3P GAIN WILD-TYPE  162  378
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              23               162
  MALE                62               378
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    59  21
  3P GAIN WILD-TYPE 386  98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     59   21
  3P GAIN WILD-TYPE  386   98
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               59               386
  YES              21                98
[1] 2 2
[1] FALSE
D5V9, continuous
D5V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED      18                         4
  3P GAIN WILD-TYPE   116                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           0    50
  3P GAIN WILD-TYPE                                         1   342
D5V11, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                                  18               116
  BLACK OR AFRICAN AMERICAN                               4                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  50               342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     4  46
  3P GAIN WILD-TYPE   7 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   46
  3P GAIN WILD-TYPE    7  358
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 7
  NOT HISPANIC OR LATINO              46               358
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    99  66
  3Q GAIN WILD-TYPE 255 179
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              165               434 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               66               179 
$`3Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 
       60.39         4.31        35.97        27.12         5.16        47.05 
TCGA-CG-5727 TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GO 
       79.07        27.35        31.27        58.55         7.63        16.24 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 
        7.69        33.27        35.21         0.85         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A97H TCGA-JY-A93C TCGA-JY-A93E 
        3.88         0.53        17.03        14.50        23.18        25.22 
TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S 
        0.30        47.93         3.32         3.16         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.60         3.75        55.50         2.66        16.47        13.22 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
        8.71        13.41        52.57        10.85        10.36        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A1 
       12.43        13.41        13.38        13.15        12.59        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-R6-A6DN 
       12.33        10.52        12.33        13.18        12.85         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC 
        7.59         5.06        53.95        12.69        20.38         3.42 
TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
        9.27        22.82        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 
       33.70        52.27        18.05        11.24         9.17        41.23 
TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-BR-4255 TCGA-BR-4257 
       14.37         1.32        19.73        11.70         4.08         9.67 
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 
        6.18        34.68         9.17        30.90        21.90        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 
       28.73         3.45         8.05         2.20        15.58        31.10 
TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-A4J4 
       26.33        14.79        25.18        12.79        27.12         0.53 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 
       32.52        20.65        20.42        13.02        13.18        11.21 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-4472 
        7.17        12.33        15.95         7.99        12.03        12.00 
TCGA-CG-4477 TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-A4YU 
       30.97        12.03        18.54        15.98        24.72        16.44 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 
       11.24        22.29        21.27        14.07        22.29        26.47 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4H0 
       24.26        24.20        22.75        25.81         8.98         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4HD TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU 
       12.95        29.00        33.40         6.44        10.62        11.70 
TCGA-KB-A6F7 TCGA-R5-A7ZR TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT 
       63.62         6.08        37.91       115.69        35.61        48.79 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PJ 
       13.02        18.48        43.36        21.73         7.73         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E 
       17.85        23.41        13.35        64.57        73.41        21.83 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA6A 
        9.73         9.04         2.01         4.54        21.04        38.93 
TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       54.12        27.55         0.79 

$`3Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 
       19.99        22.82         0.36        20.02        21.99        22.98 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF 
       16.24         0.23        20.15         9.86        26.93        25.78 
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       14.30         5.92        13.94         8.94         4.21        32.45 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
       20.78        20.12         9.30         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D 
       68.02         3.68        41.52        47.38        21.70        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       21.01        18.35         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH 
       29.00         7.43        25.12         7.40         3.02        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.48        13.55         7.76         5.49        21.37        83.24 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49W 
       46.09         5.92        12.66        12.33        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.62        12.46        12.85        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       25.25        12.00        12.23        12.03        13.18        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
        0.13        12.03        12.26        33.11         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        2.30         7.00         5.29        16.44        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7I 
       25.81        27.09         1.55        18.18        46.19        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-3M-AB46 
       18.21        25.08         3.42         2.10         2.66        58.03 
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.34         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       39.78        18.15         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 
        0.56        29.42         2.66        19.96         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 
       13.08         0.26        22.19        17.52         0.95         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8590 
        3.72         5.39         9.21        20.22         1.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        13.51         0.46         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8524 
        5.13        13.41        13.15        13.35        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.59        12.53        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 
       12.62        20.02         3.02        27.02         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
       54.08         4.01        14.01        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01        18.97         7.07         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        20.91        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        12.33        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       19.53        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       22.82        21.07         0.76        24.30         5.59        22.68 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
        3.25        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        6.58        20.25         0.26        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        13.35        19.53         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H 
        6.51        15.75        13.51         2.53         5.56        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13        16.67       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
        5.46        13.25        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91A 
        1.87         9.27        15.65        29.59        14.33        39.45 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 
       42.64        60.85         9.50        55.56        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        66.81         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        28.41        32.94        17.13        26.04        16.14 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              0.3               0.0 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           115.69            122.30 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           13.410            13.975 
[1] "0.3 - 115.7 (13.4)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         2        5       12        8        24        23
  3Q GAIN WILD-TYPE       8       16       35       25        63        64
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED          14         20         20         17       10
  3Q GAIN WILD-TYPE        14         75         52         29       39
                   vv
clus                STAGE IVA
  3Q GAIN MUTATED           3
  3Q GAIN WILD-TYPE         1
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 5                16
  STAGE IB                12                35
  STAGE II                 8                25
  STAGE IIA               24                63
  STAGE IIB               23                64
  STAGE III               14                14
  STAGE IIIA              20                75
  STAGE IIIB              20                52
  STAGE IIIC              17                29
  STAGE IV                10                39
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3Q GAIN MUTATED      16  34  78  33
  3Q GAIN WILD-TYPE    39 102 205  91
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              16                39
  T2                 34               102
  T3                 78               205
  T4                 33                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q GAIN MUTATED    54  53  22  28
  3Q GAIN WILD-TYPE 153 134  76  68
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              54               153
  N1              53               134
  N2              22                76
  N3              28                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   139   9
  3Q GAIN WILD-TYPE 385  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    139    9
  3Q GAIN WILD-TYPE  385   30
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0             139               385
  1               9                30
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    45 125
  3Q GAIN WILD-TYPE 140 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     45  125
  3Q GAIN WILD-TYPE  140  315
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              45               140
  MALE               125               315
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   114  43
  3Q GAIN WILD-TYPE 331  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    114   43
  3Q GAIN WILD-TYPE  331   76
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO              114               331
  YES              43                76
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED      41                         8
  3Q GAIN WILD-TYPE    93                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           0    96
  3Q GAIN WILD-TYPE                                         1   296
D6V11, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                                  41                93
  BLACK OR AFRICAN AMERICAN                               8                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  96               296
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5  97
  3Q GAIN WILD-TYPE   6 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5   97
  3Q GAIN WILD-TYPE    6  307
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 6
  NOT HISPANIC OR LATINO              97               307
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    23  14
  4P GAIN WILD-TYPE 331 231
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               37               562 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               231 
$`4P GAIN MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-CG-4475 TCGA-VQ-A8PU TCGA-IG-A3YB TCGA-IG-A5S3 
       18.28         4.31        22.98        27.35         2.63        23.41 
TCGA-JY-A6F8 TCGA-L5-A4ON TCGA-L5-A8NE TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A5U5 
      122.10        18.35        55.50        52.57        10.85         4.47 
TCGA-LN-A7HY TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-VR-A8EO TCGA-X8-AAAR 
       12.03        38.40        53.95         9.30        25.81        18.21 
TCGA-XP-A8T6 TCGA-Z6-AAPN TCGA-BR-8484 TCGA-BR-A4IY TCGA-CD-8528 TCGA-CG-4443 
       25.08         2.66        25.18        12.89        12.33        29.98 
TCGA-CG-5720 TCGA-CG-5722 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-A6EV TCGA-D7-A6F2 
        0.99         0.99        12.66        20.91        11.24        15.65 
TCGA-HU-A4GH TCGA-IN-7806 TCGA-IN-A7NT TCGA-VQ-A8PM TCGA-VQ-A91Q TCGA-VQ-A92D 
       11.77        36.36        10.62         1.87        20.81        66.81 
TCGA-VQ-AA6K 
       12.43 

$`4P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        21.99        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        26.93        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        83.24        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       16.31         7.04         6.35        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.10         1.32        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        1.48        27.55        28.57         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       12.10        12.76        12.59        12.53         7.17        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         6.02       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        22.29         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        33.40         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
        2.53         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70        17.85         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.99              0.00 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            122.1             122.3 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            18.21             13.87 
[1] "1.0 - 122.1 (18.2)" "0.0 - 122.3 (13.9)"
[1] "hr=" "1.2"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         1        2        3        0         3        10
  4P GAIN WILD-TYPE       9       19       44       33        84        77
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           1          7          0          1        4
  4P GAIN WILD-TYPE        27         88         72         45       45
                   vv
clus                STAGE IVA
  4P GAIN MUTATED           0
  4P GAIN WILD-TYPE         4
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 2                19
  STAGE IB                 3                44
  STAGE II                 0                33
  STAGE IIA                3                84
  STAGE IIB               10                77
  STAGE III                1                27
  STAGE IIIA               7                88
  STAGE IIIB               0                72
  STAGE IIIC               1                45
  STAGE IV                 4                45
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4P GAIN MUTATED       5   6  16   6
  4P GAIN WILD-TYPE    50 130 267 118
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               5                50
  T2                  6               130
  T3                 16               267
  T4                  6               118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P GAIN MUTATED    13  13   4   3
  4P GAIN WILD-TYPE 194 174  94  93
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              13               194
  N1              13               174
  N2               4                94
  N3               3                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"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    27   2
  4P GAIN WILD-TYPE 497  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     27    2
  4P GAIN WILD-TYPE  497   37
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              27               497
  1               2                37
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6  31
  4P GAIN WILD-TYPE 179 409
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6   31
  4P GAIN WILD-TYPE  179  409
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6               179
  MALE                31               409
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    24   8
  4P GAIN WILD-TYPE 421 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     24    8
  4P GAIN WILD-TYPE  421  111
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               24               421
  YES               8               111
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED       5                         2
  4P GAIN WILD-TYPE   129                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0    25
  4P GAIN WILD-TYPE                                         1   367
D7V11, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                                   5               129
  BLACK OR AFRICAN AMERICAN                               2                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  25               367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     2  19
  4P GAIN WILD-TYPE   9 385
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2   19
  4P GAIN WILD-TYPE    9  385
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              19               385
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    16  14
  4Q GAIN WILD-TYPE 338 231
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               30               569 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               231 
$`4Q GAIN MUTATED`
TCGA-CG-4475 TCGA-VQ-A8PU TCGA-IG-A5S3 TCGA-JY-A6F8 TCGA-L5-A43H TCGA-L5-A4ON 
       22.98        27.35        23.41       122.10         0.30        18.35 
TCGA-L5-A8NE TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HY 
       55.50        52.57        10.85        15.52        11.54        12.03 
TCGA-R6-A6Y0 TCGA-V5-A7RC TCGA-VR-A8EO TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-BR-8484 
       53.95         3.42        25.81        18.21         2.66        25.18 
TCGA-CG-5720 TCGA-CG-5722 TCGA-D7-5578 TCGA-D7-A6EV TCGA-HJ-7597 TCGA-HU-8249 
        0.99         0.99        12.66        11.24        26.47        28.96 
TCGA-IN-7806 TCGA-RD-A8N5 TCGA-VQ-A8PM TCGA-VQ-A91Q TCGA-VQ-A92D TCGA-VQ-A94T 
       36.36        57.44         1.87        20.81        66.81        11.24 

$`4Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        21.99        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF 
       16.24         0.23        20.15         9.86        26.93        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        3.88         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        21.01        47.93         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       83.24        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.76        12.59        22.39        12.85        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        5.29        16.44        15.35         9.27         8.98        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
       14.79         7.36        25.05         3.72         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         6.02       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        18.15        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.80        21.17        14.07        15.68        33.40         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       15.75        13.51         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO 
       22.19         2.50        12.79         2.70        17.85         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 
        5.72        21.04         2.66        42.54        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
              0.3               0.0 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            122.1             122.3 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            19.58             13.78 
[1] "0.3 - 122.1 (19.6)" "0.0 - 122.3 (13.8)"
[1] "hr=" "1.1"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         1        0        3        0         5         6
  4Q GAIN WILD-TYPE       9       21       44       33        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           2          5          1          0        3
  4Q GAIN WILD-TYPE        26         90         71         46       46
                   vv
clus                STAGE IVA
  4Q GAIN MUTATED           0
  4Q GAIN WILD-TYPE         4
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                21
  STAGE IB                 3                44
  STAGE II                 0                33
  STAGE IIA                5                82
  STAGE IIB                6                81
  STAGE III                2                26
  STAGE IIIA               5                90
  STAGE IIIB               1                71
  STAGE IIIC               0                46
  STAGE IV                 3                46
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4Q GAIN MUTATED       3   7  14   3
  4Q GAIN WILD-TYPE    52 129 269 121
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               3                52
  T2                  7               129
  T3                 14               269
  T4                  3               121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q GAIN MUTATED    10  10   5   2
  4Q GAIN WILD-TYPE 197 177  93  94
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              10               197
  N1              10               177
  N2               5                93
  N3               2                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    23   1
  4Q GAIN WILD-TYPE 501  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     23    1
  4Q GAIN WILD-TYPE  501   38
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              23               501
  1               1                38
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5  25
  4Q GAIN WILD-TYPE 180 415
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5   25
  4Q GAIN WILD-TYPE  180  415
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               5               180
  MALE                25               415
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    21   6
  4Q GAIN WILD-TYPE 424 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     21    6
  4Q GAIN WILD-TYPE  424  113
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               21               424
  YES               6               113
[1] 2 2
[1] FALSE
D8V9, continuous
D8V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED       4                         2
  4Q GAIN WILD-TYPE   130                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0    19
  4Q GAIN WILD-TYPE                                         1   373
D8V11, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                                   4               130
  BLACK OR AFRICAN AMERICAN                               2                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  19               373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0  16
  4Q GAIN WILD-TYPE  11 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   16
  4Q GAIN WILD-TYPE   11  388
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              16               388
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   108  64
  5P GAIN WILD-TYPE 246 181
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              172               427 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               64               181 
$`5P GAIN MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG 
       18.28         4.31         8.94        19.99         0.36        35.97 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G 
        5.16        47.05        21.99        22.98         0.23        20.15 
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC 
       14.30         5.92        32.45        33.27         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD 
       18.64         0.79        23.41        14.50        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OH 
        3.68        47.38        31.56        25.22         0.30        32.61 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93         3.32         7.17         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NV 
        7.13        15.48        55.50        12.92        13.55        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49Y 
       10.85        10.36        13.41        13.38        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59        12.59        12.85        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-RE-A7BO 
       13.18        12.85         5.06        16.31        53.95         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
       20.38         3.42        27.09        28.11        33.70        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.05        11.24        15.91        25.08        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-BR-4187 TCGA-BR-7197 
        2.10         1.32         2.66        19.73         4.64         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8060 
       35.24        33.63        39.78        18.15         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8363 
        0.69         8.05        29.42         2.66        15.58         0.26 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
       17.52        26.33        14.79         9.21        20.22        24.79 
TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 
        8.22        20.65        13.18        12.76        12.59        12.33 
TCGA-CD-A486 TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4455 
        6.31        11.61         7.99        54.08        14.01        12.03 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 
       18.97         7.07        12.00        36.00         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 
       15.02         4.01        20.91        10.26        15.22        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.31        24.72        14.66        11.31        22.29        15.65 
TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-8099 TCGA-HF-7132 TCGA-HU-8238 TCGA-HU-8245 
        0.62        19.53        17.06        77.29         1.51        18.15 
TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H0 
       28.96        24.30         3.25        22.75        25.81         2.10 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 
       23.80        33.40         6.51        10.62        11.70         5.56 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
       14.04        45.67        18.21        57.44         8.94        35.61 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PK 
        5.46        13.25        18.48        43.36        21.73        17.85 
TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A 
       39.45         9.50        55.56        11.24        43.66        38.93 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       54.12        16.14        27.55        12.43 

$`5P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T 
       15.68        60.39        34.85        24.00         4.70        22.82 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU 
       27.12        20.02        79.07        16.24         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       26.93        25.78        31.27        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24         4.21         7.69        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 
       20.78         3.88         9.30         0.53        17.03        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FG 
        9.96        14.86         4.67        12.16       122.10        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        24.03         6.28         3.16        30.25 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX 
       26.33        21.01        18.35         1.38        58.59         7.43 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75         3.02         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L 
        8.71        13.41        83.24        46.09         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.66        12.43        12.33        13.15        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.62        12.49        12.76        22.39        15.52        11.54 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       25.25        10.52        13.38         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         7.82         8.02         7.59         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         2.30        12.69 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ 
       22.82        12.43         1.55        18.31         8.12        18.18 
TCGA-VR-AA4D TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-3M-AB46 TCGA-B7-5816 
       46.19         9.17        18.21        41.23        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       21.90        36.16        35.84        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
       29.56        33.21        37.25        14.43        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       32.25         0.56        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 
       31.10        13.08        22.19         0.95         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        20.88        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51         0.46        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       16.14         5.13        13.41        13.02        13.15        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       11.21        12.10        12.53         7.17        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 
        8.05         4.01        29.98        19.07         0.00         9.01 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
       30.97         6.97         1.02         0.99         6.02       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 
       17.85        13.35        17.19        15.98        12.79        12.33 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        11.44        20.32         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       11.38         3.48        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       30.51        26.47         5.92        24.39        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76         5.59        24.26        22.68        24.20 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         0.26        12.95        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
        6.74        12.59        15.75        13.51         2.53        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64        36.95         3.72        19.73         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       71.38        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       13.02        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        14.33        73.41        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       60.85         9.73         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 
       18.41        28.41        32.94        17.13        26.04        17.26 
TCGA-ZQ-A9CR 
        0.79 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.23              0.00 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            77.29            122.30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            13.78             13.94 
[1] "0.2 - 77.3 (13.8)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         1        4       14       10        28        24
  5P GAIN WILD-TYPE       9       17       33       23        59        63
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED          11         26         16         15       16
  5P GAIN WILD-TYPE        17         69         56         31       33
                   vv
clus                STAGE IVA
  5P GAIN MUTATED           1
  5P GAIN WILD-TYPE         3
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 4                17
  STAGE IB                14                33
  STAGE II                10                23
  STAGE IIA               28                59
  STAGE IIB               24                63
  STAGE III               11                17
  STAGE IIIA              26                69
  STAGE IIIB              16                56
  STAGE IIIC              15                31
  STAGE IV                16                33
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5P GAIN MUTATED      10  42  96  23
  5P GAIN WILD-TYPE    45  94 187 101
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              10                45
  T2                 42                94
  T3                 96               187
  T4                 23               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P GAIN MUTATED    58  56  27  27
  5P GAIN WILD-TYPE 149 131  71  69
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              58               149
  N1              56               131
  N2              27                71
  N3              27                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   144  13
  5P GAIN WILD-TYPE 380  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    144   13
  5P GAIN WILD-TYPE  380   26
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             144               380
  1              13                26
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    50 129
  5P GAIN WILD-TYPE 135 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     50  129
  5P GAIN WILD-TYPE  135  311
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              50               135
  MALE               129               311
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   127  33
  5P GAIN WILD-TYPE 318  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    127   33
  5P GAIN WILD-TYPE  318   86
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              127               318
  YES              33                86
[1] 2 2
[1] FALSE
D9V9, continuous
D9V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED      39                         6
  5P GAIN WILD-TYPE    95                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           0   110
  5P GAIN WILD-TYPE                                         1   282
D9V11, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                                  39                95
  BLACK OR AFRICAN AMERICAN                               6                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 110               282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3 105
  5P GAIN WILD-TYPE   8 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  105
  5P GAIN WILD-TYPE    8  299
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO             105               299
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    41  20
  5Q GAIN WILD-TYPE 313 225
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               61               538 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               225 
$`5Q GAIN MUTATED`
TCGA-L5-A43M TCGA-L5-A4OI TCGA-KB-A93G TCGA-IG-A3I8 TCGA-JY-A93E TCGA-L5-A43H 
        8.94        19.99        20.15        33.27        25.22         0.30 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A88S TCGA-L5-A8NH TCGA-L7-A6VZ TCGA-LN-A49Y 
       32.61         3.32        15.48        12.92        10.36        12.46 
TCGA-LN-A4A1 TCGA-LN-A4MR TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-R6-A6KZ 
       12.59        13.22        12.00        12.23        12.03         5.06 
TCGA-R6-A6L4 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-AA7B TCGA-VR-AA7I TCGA-BR-7715 
       16.31         7.00         3.42        11.24        15.91        33.63 
TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-A4PD TCGA-CD-8524 
        8.05        15.58        17.52        26.33        20.65        12.76 
TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5725 
        6.31         7.99        12.03        18.97        12.00        15.02 
TCGA-CG-5730 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6F2 TCGA-FP-7829 
        4.01        15.22        24.72        14.66        15.65        19.53 
TCGA-FP-8099 TCGA-HF-7132 TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4H0 
       17.06        77.29         1.51        18.15        28.96         2.10 
TCGA-HU-A4H5 TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-RD-A8N5 
       23.80         6.51        10.62        11.70         5.56        57.44 
TCGA-RD-A8N9 TCGA-VQ-A8E0 TCGA-VQ-A91X TCGA-VQ-A94T TCGA-VQ-AA6F TCGA-VQ-AA6I 
       35.61        18.48         9.50        11.24        54.12        16.14 
TCGA-VQ-AA6K 
       12.43 

$`5Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
        0.23         9.86        27.35        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       31.56        24.03         6.28         3.16        30.25        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
       58.59         4.90        29.00         7.13         7.43         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.62        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        12.33         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       10.52        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30        12.69        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        18.05         9.17 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        32.25         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19         0.95         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       19.07         0.00         9.01         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       12.03        28.96        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         5.92        24.39 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         0.26        12.95        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.44         6.74        12.59        15.75        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       63.62        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 
       37.91        40.64       115.69       116.38        71.38         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        27.55        17.26         0.79 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              0.3               0.0 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            77.29            122.30 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           13.220            13.975 
[1] "0.3 - 77.3 (13.2)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         1        0        8        4        12         5
  5Q GAIN WILD-TYPE       9       21       39       29        75        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           3          5          8          7        5
  5Q GAIN WILD-TYPE        25         90         64         39       44
                   vv
clus                STAGE IVA
  5Q GAIN MUTATED           0
  5Q GAIN WILD-TYPE         4
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                21
  STAGE IB                 8                39
  STAGE II                 4                29
  STAGE IIA               12                75
  STAGE IIB                5                82
  STAGE III                3                25
  STAGE IIIA               5                90
  STAGE IIIB               8                64
  STAGE IIIC               7                39
  STAGE IV                 5                44
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5Q GAIN MUTATED       3  15  36   7
  5Q GAIN WILD-TYPE    52 121 247 117
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               3                52
  T2                 15               121
  T3                 36               247
  T4                  7               117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q GAIN MUTATED    25  13   9  13
  5Q GAIN WILD-TYPE 182 174  89  83
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              25               182
  N1              13               174
  N2               9                89
  N3              13                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    51   4
  5Q GAIN WILD-TYPE 473  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     51    4
  5Q GAIN WILD-TYPE  473   35
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              51               473
  1               4                35
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    16  48
  5Q GAIN WILD-TYPE 169 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     16   48
  5Q GAIN WILD-TYPE  169  392
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              16               169
  MALE                48               392
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    48  11
  5Q GAIN WILD-TYPE 397 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     48   11
  5Q GAIN WILD-TYPE  397  108
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               48               397
  YES              11               108
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED      14                         2
  5Q GAIN WILD-TYPE   120                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    38
  5Q GAIN WILD-TYPE                                         1   354
D10V11, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                                  14               120
  BLACK OR AFRICAN AMERICAN                               2                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  38               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  39
  5Q GAIN WILD-TYPE  11 365
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   39
  5Q GAIN WILD-TYPE   11  365
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              39               365
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    57  54
  6P GAIN WILD-TYPE 297 191
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              111               488 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               54               191 
$`6P GAIN MUTATED`
TCGA-L5-A8NT TCGA-CG-4460 TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK 
       27.12        21.99        25.78        31.27        14.30         7.63 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD 
       13.94        16.24         3.88         4.67       122.10        68.02 
TCGA-L5-A43E TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
       30.25        47.93        58.59        15.48         2.60         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NQ 
        3.02        55.50         2.66        12.92         5.49        21.37 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4MQ 
       10.85        10.36        10.45        13.15        12.62        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.00        12.23        13.18        12.26        16.31         7.04 
TCGA-R6-A8W5 TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4183 
       15.78        15.91         2.10        58.03        11.01         6.61 
TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 
        6.97         4.08         9.67         9.17         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 
       33.63        18.15        28.73        11.44        29.42         2.66 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
       14.04        14.79        25.18         9.21        20.22        24.79 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-A486 TCGA-CD-A487 
       20.88        10.68        20.42        13.02         6.31        12.30 
TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 
       11.61         7.99        54.08        12.03        18.97        30.97 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        10.26        15.22        12.36        11.31        12.33 
TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7735 
       14.66        14.27        11.24        22.29         7.99         3.48 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.56         5.52        28.96        25.81        23.84        21.17 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RS TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        3.39        18.38        12.59        14.04        45.67        18.21 
TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.61        37.91       115.69         8.94        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91U 
       18.48        22.19         2.70        17.85        18.74         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A94O 
        9.50         9.73        21.04 

$`6P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GJ 
        0.23        20.15         9.86        27.35        26.93        58.55 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        5.92         8.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE 
        9.96        14.86        14.50        12.16        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.13         7.43        25.12         7.40 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR 
       13.48        16.47        13.55        13.22         7.76         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M 
       13.41        83.24        52.57        46.09         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.38        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        25.25        10.52        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.38         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59         5.06        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 
       11.70        19.56         9.47         9.44         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       18.35        30.90         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       44.94        21.90        36.16        35.84        39.78        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         5.39         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        9.86         8.22        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
       12.82        12.43        11.31        12.43         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        1.02         8.05         4.01        14.01        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01         7.07        12.00         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       18.84        18.54        18.61        17.85        13.35        15.98 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.79        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        26.43        11.31        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 
       17.06        59.54         5.03        13.58         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       29.00        23.80        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.45        18.81        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
        2.53         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       19.73         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         5.13        16.67       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92        48.79         5.46        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.50        12.79         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        20.81        32.88 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       42.64        60.85        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        66.81         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.56              0.00 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            122.1             122.3 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            13.18             14.07 
[1] "0.6 - 122.1 (13.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         4        4       13        6        13        16
  6P GAIN WILD-TYPE       6       17       34       27        74        71
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           7         18         12          5       11
  6P GAIN WILD-TYPE        21         77         60         41       38
                   vv
clus                STAGE IVA
  6P GAIN MUTATED           3
  6P GAIN WILD-TYPE         1
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  4                 6
  STAGE IA                 4                17
  STAGE IB                13                34
  STAGE II                 6                27
  STAGE IIA               13                74
  STAGE IIB               16                71
  STAGE III                7                21
  STAGE IIIA              18                77
  STAGE IIIB              12                60
  STAGE IIIC               5                41
  STAGE IV                11                38
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6P GAIN MUTATED      12  32  51  18
  6P GAIN WILD-TYPE    43 104 232 106
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1              12                43
  T2                 32               104
  T3                 51               232
  T4                 18               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P GAIN MUTATED    41  34  20  17
  6P GAIN WILD-TYPE 166 153  78  79
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              41               166
  N1              34               153
  N2              20                78
  N3              17                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    95   9
  6P GAIN WILD-TYPE 429  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     95    9
  6P GAIN WILD-TYPE  429   30
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              95               429
  1               9                30
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    35  83
  6P GAIN WILD-TYPE 150 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     35   83
  6P GAIN WILD-TYPE  150  357
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              35               150
  MALE                83               357
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    90  20
  6P GAIN WILD-TYPE 355  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     90   20
  6P GAIN WILD-TYPE  355   99
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               90               355
  YES              20                99
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED      21                         5
  6P GAIN WILD-TYPE   113                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           1    75
  6P GAIN WILD-TYPE                                         0   317
D11V11, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                                  21               113
  BLACK OR AFRICAN AMERICAN                               5                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  75               317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2  75
  6P GAIN WILD-TYPE   9 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2   75
  6P GAIN WILD-TYPE    9  329
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              75               329
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    46  48
  6Q GAIN WILD-TYPE 308 197
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               94               505 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               197 
$`6Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A8NT TCGA-CG-4460 TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK 
       60.39        27.12        21.99        31.27        14.30         7.63 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43E 
       13.94        16.24         3.88       122.10        68.02        30.25 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       15.48         2.60         3.02        55.50         2.66        12.92 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49X 
       21.37        10.85        10.36        10.45        13.15        12.62 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-R6-A6L4 
       12.33         4.47        12.23        13.18        12.26        16.31 
TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-B7-A5TJ 
        7.04        15.78        15.91         2.10        58.03        11.01 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-7197 TCGA-BR-7704 
        6.61         6.97         4.08         9.67         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 
       33.63        18.15        28.73        11.44        29.42         2.66 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
       14.04        14.79        25.18         9.21        20.22        24.79 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CD-A486 TCGA-CG-4436 
       20.88        10.68         0.72        13.02         6.31         7.99 
TCGA-CG-4438 TCGA-CG-4466 TCGA-CG-4477 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 
       54.08        18.97        30.97        10.26        15.22        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-EQ-8122 TCGA-FP-7735 
       11.31        12.33        14.27        11.24         7.99         3.48 
TCGA-FP-A4BF TCGA-HU-A4GT TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
        5.52         6.51        21.17         3.45         3.39        18.38 
TCGA-IN-A6RS TCGA-MX-A666 TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A8N6 TCGA-VQ-A8DV 
       12.59        14.04        45.67         8.61         8.94        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91N 
       13.02        18.48        22.19         2.70        17.85        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A94R 
       32.88         1.71         9.50        42.54 

$`6Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        35.97         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GJ 
       20.15         9.86        27.35        26.93        25.78        58.55 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        5.92         8.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.43        25.12         7.40         3.75        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        46.09         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        15.35        12.59        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.85        15.52        11.54        13.22        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.03        13.18        12.33        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         5.06        38.40         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         9.44         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       44.94        21.90        36.16        35.84        39.78        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         5.39         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        9.86         8.22        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         1.02         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       29.98        19.07        12.03         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 
       17.85        13.35        17.19        15.98        12.79        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM 
       17.06        59.54         5.03        13.58         0.56         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL 
       15.68        33.40        36.36        18.81        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.44         6.74         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       15.75        13.51         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       36.95         3.72        19.73        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79         5.46        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        12.79         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W 
       11.70        21.83        61.22        20.81        42.64        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T 
        6.58         5.72        66.81        21.04         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.72              0.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            122.1             122.3 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            13.02             14.33 
[1] "0.7 - 122.1 (13.0)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         5        3       11        5        11        11
  6Q GAIN WILD-TYPE       5       18       36       28        76        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           5         15          9          3       12
  6Q GAIN WILD-TYPE        23         80         63         43       37
                   vv
clus                STAGE IVA
  6Q GAIN MUTATED           3
  6Q GAIN WILD-TYPE         1
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  5                 5
  STAGE IA                 3                18
  STAGE IB                11                36
  STAGE II                 5                28
  STAGE IIA               11                76
  STAGE IIB               11                76
  STAGE III                5                23
  STAGE IIIA              15                80
  STAGE IIIB               9                63
  STAGE IIIC               3                43
  STAGE IV                12                37
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6Q GAIN MUTATED      12  26  39  18
  6Q GAIN WILD-TYPE    43 110 244 106
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1              12                43
  T2                 26               110
  T3                 39               244
  T4                 18               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q GAIN MUTATED    36  30  13  15
  6Q GAIN WILD-TYPE 171 157  85  81
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              36               171
  N1              30               157
  N2              13                85
  N3              15                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    77  11
  6Q GAIN WILD-TYPE 447  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     77   11
  6Q GAIN WILD-TYPE  447   28
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              77               447
  1              11                28
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    27  73
  6Q GAIN WILD-TYPE 158 367
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     27   73
  6Q GAIN WILD-TYPE  158  367
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              27               158
  MALE                73               367
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    75  20
  6Q GAIN WILD-TYPE 370  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     75   20
  6Q GAIN WILD-TYPE  370   99
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               75               370
  YES              20                99
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED      17                         5
  6Q GAIN WILD-TYPE   117                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           1    63
  6Q GAIN WILD-TYPE                                         0   329
D12V11, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                                  17               117
  BLACK OR AFRICAN AMERICAN                               5                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  63               329
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  62
  6Q GAIN WILD-TYPE   9 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   62
  6Q GAIN WILD-TYPE    9  342
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              62               342
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   176 118
  7P GAIN WILD-TYPE 178 127
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              294               305 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              118               127 
$`7P GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
       60.39         4.31        24.00         4.70         0.36        35.97 
TCGA-L5-A8NT TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       27.12        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
        9.86        26.93        25.78         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC 
       16.24        32.45         7.69        35.21         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       18.64         0.53        17.03         0.79        23.41        14.50 
TCGA-JY-A6FE TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
        3.68        21.70        23.18        25.22         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.30        26.33        32.61        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
        3.16        58.59         4.90         7.13        15.48         2.60 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.75         3.02         2.66        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       13.22         5.49         8.71        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.36         5.92        12.43        13.41        13.38        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.59        12.85        12.33        13.22        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW 
       12.00        12.33         0.13        12.85        12.26         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       53.95         9.30         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       27.09         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       46.19        11.24        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ 
        2.10         1.32         2.66        19.73        11.70        11.01 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6566 
        6.97         4.64         9.67        17.29         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       25.61        18.05        40.21         9.21        35.24        33.63 
TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 
       18.15         3.45        29.56        33.21        14.43         0.69 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        29.42         2.20        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 
       13.08         0.95         3.32        14.79         7.36         5.39 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       20.22         1.12        32.58         9.86         8.22        10.68 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 
       13.87        34.98         1.48        12.89         0.72         0.53 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 
       32.52        13.51        20.65        20.42        21.44        13.02 
TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       13.18        12.10        12.39        15.39        12.07        12.43 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 
        6.31        12.43        11.61         6.58        12.20        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4469 
       27.02        15.95         7.99         4.01        14.01         7.07 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5733 TCGA-CG-5734 
       12.00        36.00        12.03        28.96        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 
       12.66        20.91        19.13        18.84        18.54        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       10.26        15.22        15.98        12.36        12.33        24.72 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       17.19        18.21        14.66        21.14        20.91        16.44 
TCGA-D7-A4YX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
       36.43        22.29        15.65        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-A9TM TCGA-HF-7134 
       19.53        14.07        22.29        17.06         6.21        52.21 
TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD 
       26.47        28.96        24.30        24.26         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
       25.81         8.98         0.10        20.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       29.00        23.84        23.80        33.40         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39        18.38        13.35         6.44        12.59         6.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        5.56        63.62        37.64        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 
       74.53         6.08         8.61       122.30        57.44         8.94 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79        13.25        13.02        43.36        21.73        37.41 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PY 
       34.29        46.26         2.50        12.79        17.85        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q 
       73.41        39.45        11.70        21.83        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 
        1.71        42.64        60.85         9.50         2.01         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       21.04        42.54        11.24        43.66        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        16.14        27.55        12.43        17.26         0.79 

$`7P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         8.94        19.99        22.82 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-2H-A9GH 
        5.16        20.02        47.05        16.24        27.35        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 
       14.30        58.55         7.63         4.21        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       20.78         3.88         9.30        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        4.67        12.16       122.10        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OJ TCGA-L5-A4OM 
       47.38        31.56        24.03         6.28        21.01        47.93 
TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE 
        7.17        29.00         7.43        25.12         7.40        55.50 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L 
       13.48         7.76        21.37        13.41        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.66        12.33        13.15        12.46        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       11.54         4.47        10.52        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6XQ TCGA-R6-A8W5 
       13.38        13.18        12.03        33.11         6.35        15.78 
TCGA-R6-A8W8 TCGA-V5-A7RE TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EZ TCGA-VR-A8Q7 
        2.89        16.44        22.82        12.43        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-3M-AB46 TCGA-B7-5816 
       18.05         9.17        41.23         3.42        58.03        26.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         9.44         6.61         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       39.12        26.10        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       31.20        44.94        21.90        36.16        35.84        39.78 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 
       15.32        28.73         9.07        37.25        11.44        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 
        9.60        32.25         2.66        19.96         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19        17.52        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       11.80        31.27        25.05         3.72        25.18         9.21 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A452 
       26.73        24.79        31.96        20.88        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        6.08        27.55        28.57         8.98        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.66         0.46         1.15        16.14         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.35        11.21        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        7.17        12.33        12.30        12.59        11.64        12.82 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 
       12.30        11.31        11.77        12.62         3.02         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        8.05        54.08        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        9.01        18.97        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       69.04        25.71        20.55        18.61        17.85        13.35 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A4YV 
       12.79        11.31        16.80        19.50        14.27         5.92 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       20.32         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        7.99        21.27        11.38        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HU-8238 
        0.56         5.52        77.29        63.06        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        18.15        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GJ 
        0.76         5.59        22.68        24.20        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H6 TCGA-HU-A4H8 
       29.98         6.51         6.58         0.26        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NT 
       15.68        36.36        12.46        19.53         6.74        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG 
       11.70        15.75        13.51         2.53        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       19.73        14.04         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       35.61        16.87        19.04         5.79         0.92         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PD 
       18.48        38.14        37.22         7.73        30.97        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       22.19         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91Y 
       13.35        29.59        64.57        61.22        32.88         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       55.56         9.04        55.43         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
        2.66        18.41        28.41        17.13        26.04 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              0.1               0.0 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            122.3             122.1 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            13.71             14.04 
[1] "0.1 - 122.3 (13.7)" "0.0 - 122.1 (14.0)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         7        8       23       15        38        44
  7P GAIN WILD-TYPE       3       13       24       18        49        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED          19         40         34         25       21
  7P GAIN WILD-TYPE         9         55         38         21       28
                   vv
clus                STAGE IVA
  7P GAIN MUTATED           3
  7P GAIN WILD-TYPE         1
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  7                 3
  STAGE IA                 8                13
  STAGE IB                23                24
  STAGE II                15                18
  STAGE IIA               38                49
  STAGE IIB               44                43
  STAGE III               19                 9
  STAGE IIIA              40                55
  STAGE IIIB              34                38
  STAGE IIIC              25                21
  STAGE IV                21                28
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7P GAIN MUTATED      33  57 145  52
  7P GAIN WILD-TYPE    22  79 138  72
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              33                22
  T2                 57                79
  T3                145               138
  T4                 52                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P GAIN MUTATED    98  93  45  48
  7P GAIN WILD-TYPE 109  94  53  48
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              98               109
  N1              93                94
  N2              45                53
  N3              48                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"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   249  18
  7P GAIN WILD-TYPE 275  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    249   18
  7P GAIN WILD-TYPE  275   21
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             249               275
  1              18                21
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    71 237
  7P GAIN WILD-TYPE 114 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     71  237
  7P GAIN WILD-TYPE  114  203
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              71               114
  MALE               237               203
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   216  57
  7P GAIN WILD-TYPE 229  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    216   57
  7P GAIN WILD-TYPE  229   62
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              216               229
  YES              57                62
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED      64                        13
  7P GAIN WILD-TYPE    70                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           1   191
  7P GAIN WILD-TYPE                                         0   201
D13V11, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                                  64                70
  BLACK OR AFRICAN AMERICAN                              13                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 191               201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     8 187
  7P GAIN WILD-TYPE   3 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8  187
  7P GAIN WILD-TYPE    3  217
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                 3
  NOT HISPANIC OR LATINO             187               217
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   147  96
  7Q GAIN WILD-TYPE 207 149
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              243               356 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               96               149 
$`7Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
       60.39         4.31        24.00         4.70         0.36        35.97 
TCGA-L5-A8NT TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       27.12        22.98        79.07         0.23        20.15         9.86 
TCGA-2H-A9GF TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
       25.78         8.94        16.24        32.45         7.69        35.21 
TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FE TCGA-JY-A939 
       18.64        17.03        23.41        14.50         3.68        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        25.22         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT 
       26.33        32.61        47.93         3.32         3.16         4.90 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NL 
       15.48         2.60         3.75         3.02         2.66        13.22 
TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
        5.49        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        15.35        12.59        13.25 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.49        12.76        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A9FO 
       13.22        12.33        25.25        12.00        12.33         0.13 
TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       12.85         7.82         8.02        16.31         7.04        38.40 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW 
        3.42        15.35         9.27        27.09        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR 
       28.11        33.70        18.18        46.19        11.24        18.21 
TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ 
       25.08         2.10         1.32        19.73        11.70        11.01 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6565 
        6.97         4.64        18.35         9.67        17.29         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
       32.78        25.61        18.05        40.21         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8284 
       33.63        18.15        29.56        33.21        14.43         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 
        0.56        29.42         2.20        15.58         7.40        13.08 
TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8486 
        0.95         3.32        14.79         7.36         5.39        20.22 
TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A4IY TCGA-BR-A4J1 
        1.12        32.58         9.86        10.68        12.89         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5799 
        0.53        32.52        13.51        20.65        20.42        13.02 
TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       13.18        12.10        12.39        15.39        12.07        12.43 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
       12.43         6.58        12.20        20.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 
        7.99         4.01        14.01         7.07        12.00        36.00 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       12.03        28.96        21.07        12.66        20.91        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 
       18.84        18.54        17.19        10.26        15.22        24.72 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       19.50        17.19        14.66        21.14        20.91        16.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 
       22.29        15.65        14.47        72.23         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-A9TM TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8249 
       22.29        17.06         6.21        52.21        26.47        28.96 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       24.30        24.26        25.81         8.98         0.10        20.25 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-IN-8462 TCGA-IN-8663 
        2.10        12.95        29.00        23.84        18.81         3.39 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-R5-A7O7 
       13.35         6.44         6.51         5.56        63.62        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV 
       18.21         8.52        74.53         6.08         8.61       122.30 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
       57.44         8.94        48.79        13.25        13.02        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PK 
       21.73        37.41        34.29        46.26         2.50        17.85 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91Q 
       14.33        73.41        39.45        11.70        21.83        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 
        1.71        42.64        60.85         9.50         2.01         4.54 
TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       21.04        11.24        43.66        38.93        32.94        54.12 
TCGA-VQ-AA6I TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        17.26         0.79 

$`7Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         8.94        19.99        22.82 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-VQ-A8PU 
        5.16        20.02        47.05        21.99        16.24        27.35 
TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       26.93        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       13.94         4.21        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 
       20.12         3.88         9.30         0.53         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OJ 
       68.02        41.52        47.38        24.03         6.28        21.01 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         7.17         1.38        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
        7.43        25.12         7.40        55.50        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55         7.76        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49X 
       83.24        10.45        12.66        12.43        13.15        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A5U5 TCGA-LN-A7HV 
       12.46        12.59        12.59        22.39         4.47        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP 
       12.23        12.03        13.18        13.38        13.18        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 
       12.26        33.11         7.59         5.06         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
       15.78         2.89        16.44         8.98        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       12.43         1.55        52.27        18.05         9.17        15.91 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 
       41.23        14.37         3.42         2.66        58.03        26.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 
       19.56         9.47         9.44         6.61         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       26.10        19.89        12.16         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       44.94        21.90        36.16        35.84        39.78        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
       28.73         3.45         9.07        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 
       29.59         9.60        32.25         2.66        19.96         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
       31.10         0.26        22.19        17.52        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       14.04        11.80        31.27        25.05         3.72        25.18 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 
        7.53        26.73        24.79        31.96        20.88         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       27.55        28.57         8.98        14.17        28.34         0.66 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.35        11.21        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        7.17        12.33        12.30        12.59        11.64        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ 
        6.31        12.30        11.31        11.61        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 
        3.02         1.02         8.05        54.08        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01        18.97        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 
       65.10         4.01        69.04         7.99        25.71        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        13.35        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YV 
       11.31        12.33        16.80        18.21        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44        20.32         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8209 
        0.62         7.99        21.27        11.38        19.53        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         0.56         5.52        77.29        63.06 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        18.15        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       22.82        21.07         0.76         5.59        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT 
        3.25        22.75        11.77        21.37        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.58         0.26        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       33.40        36.36         3.45        18.38        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        4.60         9.24        11.05         5.13        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       115.69       116.38        71.38        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8P2 
       19.04         5.79         0.92         5.46        18.48        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH 
       37.22         7.73        30.97        16.31        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91Y 
       29.59        64.57        61.22        18.74        32.88         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       55.56         9.04        55.43         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
        2.66        42.54        18.41        28.41        17.13        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K 
       27.55        12.43 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.1               0.0 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            122.3             122.1 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           14.500            13.565 
[1] "0.1 - 122.3 (14.5)" "0.0 - 122.1 (13.6)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         6        8       20       15        33        29
  7Q GAIN WILD-TYPE       4       13       27       18        54        58
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED          14         31         29         24       18
  7Q GAIN WILD-TYPE        14         64         43         22       31
                   vv
clus                STAGE IVA
  7Q GAIN MUTATED           3
  7Q GAIN WILD-TYPE         1
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  6                 4
  STAGE IA                 8                13
  STAGE IB                20                27
  STAGE II                15                18
  STAGE IIA               33                54
  STAGE IIB               29                58
  STAGE III               14                14
  STAGE IIIA              31                64
  STAGE IIIB              29                43
  STAGE IIIC              24                22
  STAGE IV                18                31
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7Q GAIN MUTATED      28  50 121  40
  7Q GAIN WILD-TYPE    27  86 162  84
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              28                27
  T2                 50                86
  T3                121               162
  T4                 40                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q GAIN MUTATED    86  70  37  43
  7Q GAIN WILD-TYPE 121 117  61  53
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              86               121
  N1              70               117
  N2              37                61
  N3              43                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"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   205  15
  7Q GAIN WILD-TYPE 319  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    205   15
  7Q GAIN WILD-TYPE  319   24
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             205               319
  1              15                24
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    59 198
  7Q GAIN WILD-TYPE 126 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     59  198
  7Q GAIN WILD-TYPE  126  242
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              59               126
  MALE               198               242
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   183  47
  7Q GAIN WILD-TYPE 262  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    183   47
  7Q GAIN WILD-TYPE  262   72
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              183               262
  YES              47                72
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED      54                        11
  7Q GAIN WILD-TYPE    80                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           1   159
  7Q GAIN WILD-TYPE                                         0   233
D14V11, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                                  54                80
  BLACK OR AFRICAN AMERICAN                              11                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 159               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     7 156
  7Q GAIN WILD-TYPE   4 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7  156
  7Q GAIN WILD-TYPE    4  248
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 4
  NOT HISPANIC OR LATINO             156               248
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   138  98
  8P GAIN WILD-TYPE 216 147
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              236               363 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               98               147 
$`8P GAIN MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-CG-4460 
       18.28         4.31        19.99         0.36        35.97        21.99 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       79.07        16.24         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
       26.93        14.30         8.94        16.24         4.21        32.45 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 
       33.27        35.21        20.78        17.03        12.82         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C 
      122.10        68.02         3.68        31.56        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
       30.25         0.30        47.93        18.35         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A8NK TCGA-L5-A8NL 
        4.90         7.13         7.43         2.60        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
        7.76        21.37        13.41        10.85        10.36         5.92 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A4 
       13.41        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A6 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-R6-A6DQ 
       12.85        12.03        13.18        12.33         0.13         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE 
        5.06         7.04        15.78        12.69         7.00        16.44 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D 
       15.35        27.09        22.82         8.12        18.18        46.19 
TCGA-VR-AA7B TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TJ 
       11.24         3.42         2.10        19.73        26.70        11.01 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4255 
        9.47         6.61         6.97         4.64        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.34         9.67        34.68        15.95        13.87        13.68 
TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7707 
       19.89        30.90        31.20        44.94        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       33.63         9.07        11.44        29.59         9.60         8.05 
TCGA-BR-8297 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 
        7.40         4.31        14.04         3.32        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8591 
       25.05         5.39         9.21        20.22         9.34        28.14 
TCGA-BR-8676 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J5 
        7.53         7.53        34.98         1.48        27.55        28.34 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5803 
       32.52         0.46        20.42        16.14        13.15        11.21 
TCGA-CD-8530 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MJ 
       12.39        12.43         6.31        12.30         6.58        12.62 
TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       20.02        15.95        14.01        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5726 
        7.07        12.00        36.00         0.99        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6524 
       65.10        21.07        20.91        19.13        18.84        17.85 
TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 
       17.19        12.79        12.36        11.31        12.33        14.66 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX 
       20.91         5.92        36.43        14.76        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-F1-A448 TCGA-FP-7829 
       11.44        22.29         8.38         4.34        21.27        19.53 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       24.39        22.32        24.30        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        29.98         8.98         0.10 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.26         2.10        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NR 
       15.68         3.45         3.39        13.35        12.59         6.51 
TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       10.62        63.62        37.64        19.73         8.52        74.53 
TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
        6.08        16.67       115.69        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P2 
        5.79         0.92        48.79         5.46        13.02        38.14 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH 
        7.73        30.97        34.29        16.31        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91A 
        2.70         9.27        23.41        29.59        64.57        39.45 
TCGA-VQ-A91E TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R 
       21.83        42.64        60.85         5.72        21.04        42.54 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

$`8P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 
       22.82        27.12         5.16        20.02        47.05        22.98 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        7.69         0.85         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53         0.79        23.41         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       14.50        12.16        44.75        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       23.18        25.22         6.28        26.33        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88W 
        3.32         7.17        58.59        29.00        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
       13.48        16.47         5.49         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R 
       46.09        10.45        12.66        12.43        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       13.15        12.46        12.59        12.49        12.76        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-LN-A8I1 
       25.25        10.52        12.00        12.23        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
       16.31        38.40         6.35        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX 
        2.30        20.38         5.29         3.42         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY 
       25.81        12.43         1.55        18.31        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       52.27        18.05         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5818 
       41.23        14.37         1.32         2.66        58.03        11.70 
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4267 
       19.56         9.44         7.43        18.35         4.08         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
        9.57         6.61        17.29        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        12.16         8.98 
TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7717 
       40.21        21.90         9.21        36.16        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73         3.45        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       14.43         0.69        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       19.96         2.20        15.58         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 
        0.26        22.19        17.52         0.95        26.33        11.80 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       14.79         3.72        25.18         1.12        12.79        27.12 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       20.88         8.22        10.68        34.13        13.87         6.08 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
        0.66        13.51        20.65         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8524 
       13.41        13.02        13.18        13.35        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A 
       11.64        15.39        12.07        12.82        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.61        12.20        11.77         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05        54.08         4.01        29.98        19.07 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        9.01        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
      105.07        12.03         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 
       12.66        20.55        18.54        18.61        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       15.22        15.98        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6ET 
       18.21        21.14        14.27        16.44        13.78        26.43 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       20.32        15.65        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23        11.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7133 
       17.06        59.54         5.03        13.58         0.56        63.06 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        18.15        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GT TCGA-HU-A4GU 
        0.76         5.59        11.77        21.37         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       20.25        12.95        21.17        33.40        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU 
       18.38        12.46        19.53         6.44         6.74        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53         5.56        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       14.04        45.67        18.21         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         5.13       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       71.38        57.44         8.94        13.25        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PK 
       21.73        37.41        37.22        46.26         2.50        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
        1.87        15.65        13.35        14.33        73.41        11.70 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X 
       61.22        18.74        20.81        32.88         1.71         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        6.58        66.81         2.66        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       16.14        27.55        12.43 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.00              0.26 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            122.1             122.3 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           14.055            13.780 
[1] "0.0 - 122.1 (14.1)" "0.3 - 122.3 (13.8)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         2       10       22       14        30        39
  8P GAIN WILD-TYPE       8       11       25       19        57        48
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED          13         35         22         22       17
  8P GAIN WILD-TYPE        15         60         50         24       32
                   vv
clus                STAGE IVA
  8P GAIN MUTATED           2
  8P GAIN WILD-TYPE         2
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                10                11
  STAGE IB                22                25
  STAGE II                14                19
  STAGE IIA               30                57
  STAGE IIB               39                48
  STAGE III               13                15
  STAGE IIIA              35                60
  STAGE IIIB              22                50
  STAGE IIIC              22                24
  STAGE IV                17                32
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8P GAIN MUTATED      22  56 108  49
  8P GAIN WILD-TYPE    33  80 175  75
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              22                33
  T2                 56                80
  T3                108               175
  T4                 49                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P GAIN MUTATED    82  70  35  43
  8P GAIN WILD-TYPE 125 117  63  53
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              82               125
  N1              70               117
  N2              35                63
  N3              43                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"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   207  15
  8P GAIN WILD-TYPE 317  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    207   15
  8P GAIN WILD-TYPE  317   24
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             207               317
  1              15                24
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    87 161
  8P GAIN WILD-TYPE  98 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     87  161
  8P GAIN WILD-TYPE   98  279
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              87                98
  MALE               161               279
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   176  46
  8P GAIN WILD-TYPE 269  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    176   46
  8P GAIN WILD-TYPE  269   73
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              176               269
  YES              46                73
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED      49                         7
  8P GAIN WILD-TYPE    85                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           0   159
  8P GAIN WILD-TYPE                                         1   233
D15V11, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                                  49                85
  BLACK OR AFRICAN AMERICAN                               7                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 159               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3 158
  8P GAIN WILD-TYPE   8 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3  158
  8P GAIN WILD-TYPE    8  246
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO             158               246
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   191 129
  8Q GAIN WILD-TYPE 163 116
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              320               279 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              129               116 
$`8Q GAIN MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       18.28         4.31        19.99         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       20.02        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GN 
        9.86        27.35        26.93        14.30        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A625 
       20.78         2.63        20.12         3.88        17.03        12.82 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93C 
        4.67        14.50       122.10        68.02         3.68        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OM 
       31.56        24.03         3.16        30.25         0.30        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
       18.35         3.32         1.38         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        7.43         2.60        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       21.37         8.71        13.41        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
        5.92        13.41        12.33        13.38        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 
       13.25        12.62        12.59        12.49        12.59        12.85 
TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       11.54        12.33        12.23        12.03        13.18        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DQ TCGA-R6-A6KZ 
       13.18         0.13        12.85        12.26         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        7.04        53.95        15.78        12.69         7.00        20.38 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27         8.98        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B 
       12.43         8.12        33.70        18.18        46.19        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
        9.17        15.91        41.23         3.42         2.10         1.32 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       19.73        26.70        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 
        4.64        30.90         4.08         9.34         9.67        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6707 
       15.95        13.87        17.29        13.68         9.17        19.89 
TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 
       12.16        30.90        31.20        44.94         9.21        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8060 
       35.84        33.63        39.78         9.07        29.56        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8297 
        0.69        29.59         9.60         8.05        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        6.18        13.08        26.33         4.31        14.04         3.32 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
       31.27         7.36        25.05         5.39         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8687 
       12.79         9.34        28.14         7.53        32.58         8.22 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J1 
       13.87         7.53        34.98         1.48        27.55         0.72 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5803 
       28.34        32.52         0.46        16.14        13.15        11.21 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
       12.59        12.53        12.39        15.39        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 
        6.31        12.30         6.58        12.62        20.02        15.95 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
        8.05        54.08        14.01        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5726 
        7.07        12.00        36.00         0.99        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 
       65.10         4.01        69.04        21.07        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       19.13        18.84        17.85        13.35        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8579 
       12.79        12.36        11.31        12.33        14.66        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX 
       16.44         5.92        36.43        14.76        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-EQ-5647 
       11.44        22.29        15.65         8.38         4.34         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8631 
        7.99        72.23        21.27         3.48        19.53         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        24.39        18.15        22.32         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10         6.51         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        3.45         3.39        13.35         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UJ TCGA-MX-A666 
        6.51        10.62        63.62        37.64        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BS 
       45.67        18.21         8.52        74.53         6.08        11.05 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       16.67       115.69        71.38        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       38.14         7.73        30.97        34.29        16.31        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PT 
       12.79         2.70         9.27        23.41        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A928 
       64.57        39.45        21.83        42.64        60.85         5.72 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-VQ-AA6K 
       21.04        42.54        18.41        43.66        16.14        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

$`8Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-2H-A9GF TCGA-2H-A9GH 
       22.82         5.16        47.05        22.98        25.78        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-IG-A4QT 
       58.55         7.63         5.92         0.85        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I 
        0.53         0.79        23.41         9.96        14.86        12.16 
TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC 
       44.75        41.52        47.38        21.70        25.22         6.28 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU 
       26.33        32.61        21.01         7.17        58.59        29.00 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV 
        2.66        12.92        13.48        16.47        83.24        52.57 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A3 
       10.45        12.66        12.43        13.15        12.46        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       22.39        15.52        12.33        13.22         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW 
       10.52        12.00        13.38        12.03        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 
        8.02        16.31        38.40         6.35         9.30         2.89 
TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EU 
        2.30         5.29         3.42        25.81         1.55        18.31 
TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       28.11        52.27        18.05        18.21        25.08        14.37 
TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4188 
        2.66        58.03        11.70        19.56         9.44         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6458 
       18.35         4.08         6.18         9.57         6.61        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 
       39.12        26.10        32.78        25.61        18.05         8.98 
TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       40.21        21.90        36.16        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8285 
        3.45        33.21        37.25        14.43        32.25         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8361 TCGA-BR-8363 
       29.42         2.66        19.96         2.20        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 
       22.19        17.52         0.95        11.80        14.79         3.72 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 
       25.18         1.12        27.12         6.28        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
       31.96         9.86        20.88        10.68        34.13         6.08 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       28.57        12.89         8.98        14.17         0.53         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8524 
       13.41        13.02        13.18        13.35        12.10        12.76 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 
        7.17        12.33        12.30        12.59        11.64        12.07 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4301 
       11.31        12.43        11.61        12.20        11.77         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
       27.02         1.02         7.99         4.01        29.98        19.07 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        9.01        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 
      105.07        12.03         7.99        25.71        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       18.61        10.26        15.22        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-D7-A6ET 
       17.19        18.21        21.14        14.27        13.78        26.43 
TCGA-D7-A6EZ TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7916 
       20.32        19.96         7.13        14.47        11.38        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7133 
       22.29        17.06        59.54         5.03        13.58        63.06 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4GH 
        1.51        28.96        22.82        21.07         5.59        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7806 
       21.37         6.58        20.25        12.95        21.17        36.36 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IN-AB1V 
       18.81        18.38        12.46        19.53        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-R5-A804 
       13.51         2.53         5.56        36.95         3.72         4.60 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        9.24         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
      116.38        57.44         8.94        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        37.22        46.26         2.50        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N 
       15.65        14.33        73.41        11.70        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81        32.88         1.71         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.04         2.01        55.43         4.54         6.58        66.81 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
        2.66        11.24        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       54.12        26.04        27.55 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.00              0.26 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            122.1             122.3 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           13.365            14.790 
[1] "0.0 - 122.1 (13.4)" "0.3 - 122.3 (14.8)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         3       13       26       17        44        51
  8Q GAIN WILD-TYPE       7        8       21       16        43        36
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED          18         53         32         31       22
  8Q GAIN WILD-TYPE        10         42         40         15       27
                   vv
clus                STAGE IVA
  8Q GAIN MUTATED           2
  8Q GAIN WILD-TYPE         2
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  3                 7
  STAGE IA                13                 8
  STAGE IB                26                21
  STAGE II                17                16
  STAGE IIA               44                43
  STAGE IIB               51                36
  STAGE III               18                10
  STAGE IIIA              53                42
  STAGE IIIB              32                40
  STAGE IIIC              31                15
  STAGE IV                22                27
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8Q GAIN MUTATED      28  73 154  65
  8Q GAIN WILD-TYPE    27  63 129  59
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              28                27
  T2                 73                63
  T3                154               129
  T4                 65                59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q GAIN MUTATED   108 101  47  57
  8Q GAIN WILD-TYPE  99  86  51  39
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             108                99
  N1             101                86
  N2              47                51
  N3              57                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"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   282  18
  8Q GAIN WILD-TYPE 242  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    282   18
  8Q GAIN WILD-TYPE  242   21
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             282               242
  1              18                21
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   108 229
  8Q GAIN WILD-TYPE  77 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    108  229
  8Q GAIN WILD-TYPE   77  211
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             108                77
  MALE               229               211
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   233  68
  8Q GAIN WILD-TYPE 212  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    233   68
  8Q GAIN WILD-TYPE  212   51
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              233               212
  YES              68                51
[1] 2 2
[1] FALSE
D16V9, continuous
D16V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED      73                        10
  8Q GAIN WILD-TYPE    61                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           0   212
  8Q GAIN WILD-TYPE                                         1   180
D16V11, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                                  73                61
  BLACK OR AFRICAN AMERICAN                              10                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 212               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"
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     5 223
  8Q GAIN WILD-TYPE   6 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5  223
  8Q GAIN WILD-TYPE    6  181
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 6
  NOT HISPANIC OR LATINO             223               181
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    55  20
  9P GAIN WILD-TYPE 299 225
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               75               524 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               20               225 
$`9P GAIN MUTATED`
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-CG-4444 TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GL 
        0.36        27.12        47.05         0.23        20.15         5.92 
TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A93C TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L7-A56G 
       12.82       122.10        23.18         3.32        29.00        10.85 
TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A8I0 
       10.36        13.41        12.33        13.38        12.59        13.38 
TCGA-LN-A9FQ TCGA-R6-A6L4 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-B7-A5TK 
       12.85        16.31        18.05         9.17         2.66         9.47 
TCGA-BR-6456 TCGA-BR-6707 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8080 
       17.29        19.89        35.84        33.63        33.21         9.60 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-A4J4 TCGA-BR-A4J9 
        2.66         2.20        12.79        32.58         0.53         0.46 
TCGA-BR-A4PE TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8535 TCGA-CD-A4MH TCGA-CG-4436 
       20.42        13.41        13.18        12.82        12.20         7.99 
TCGA-CG-4477 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4Z0 
       30.97        15.22        12.36        12.33        18.21        14.76 
TCGA-D7-A6EY TCGA-EQ-5647 TCGA-F1-A448 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
       11.44         0.62        21.27        77.29        52.21        30.51 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H0 
       28.96         0.76        24.26        22.75         8.98         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-8663 TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-R5-A7ZI 
       12.95        23.80         3.39         6.44        63.62        74.53 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PP 
      122.30       115.69        35.61         5.46        46.26        23.41 
TCGA-VQ-A91S TCGA-VQ-A91Z TCGA-VQ-A922 
       32.88        55.56         9.04 

$`9P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU 
       24.00         4.70        19.99        22.82        35.97         5.16 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 
       20.02        21.99        22.98        79.07        16.24         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       27.35        26.93        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
        8.71        13.41        83.24        52.57        46.09         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       10.45        12.66        12.43        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        46.19        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.24        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
       29.59        32.25         8.05         0.56        29.42        19.96 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        31.96         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
       28.34         0.66        32.52        13.51        20.65         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       21.44        16.14         5.13        13.02        13.15        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        12.00         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.98        12.79        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        13.78        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        7.13         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 
       13.58         0.56         5.52         6.21        63.06        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       21.07        24.30         5.59        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.58        20.25         0.26        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        13.35        19.53         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79         0.92        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70        17.85         1.87         9.27        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        18.74        20.81         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       60.85         9.50         9.73         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.23              0.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           122.30            116.38 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           13.410            14.025 
[1] "0.2 - 122.3 (13.4)" "0.0 - 116.4 (14.0)"
[1] "hr=" "1.8"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         1        3        9        3        12         8
  9P GAIN WILD-TYPE       9       18       38       30        75        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           2         12         10          8        5
  9P GAIN WILD-TYPE        26         83         62         38       44
                   vv
clus                STAGE IVA
  9P GAIN MUTATED           0
  9P GAIN WILD-TYPE         4
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 3                18
  STAGE IB                 9                38
  STAGE II                 3                30
  STAGE IIA               12                75
  STAGE IIB                8                79
  STAGE III                2                26
  STAGE IIIA              12                83
  STAGE IIIB              10                62
  STAGE IIIC               8                38
  STAGE IV                 5                44
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9P GAIN MUTATED       8  17  34  16
  9P GAIN WILD-TYPE    47 119 249 108
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               8                47
  T2                 17               119
  T3                 34               249
  T4                 16               108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    29  18  13  14
  9P GAIN WILD-TYPE 178 169  85  82
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              29               178
  N1              18               169
  N2              13                85
  N3              14                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"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    69   3
  9P GAIN WILD-TYPE 455  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     69    3
  9P GAIN WILD-TYPE  455   36
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              69               455
  1               3                36
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    22  56
  9P GAIN WILD-TYPE 163 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     22   56
  9P GAIN WILD-TYPE  163  384
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              22               163
  MALE                56               384
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    48  23
  9P GAIN WILD-TYPE 397  96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     48   23
  9P GAIN WILD-TYPE  397   96
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               48               397
  YES              23                96
[1] 2 2
[1] FALSE
D17V9, continuous
D17V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED      23                         2
  9P GAIN WILD-TYPE   111                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           0    42
  9P GAIN WILD-TYPE                                         1   350
D17V11, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                                  23               111
  BLACK OR AFRICAN AMERICAN                               2                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  42               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  53
  9P GAIN WILD-TYPE   9 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   53
  9P GAIN WILD-TYPE    9  351
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              53               351
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    71  34
  9Q GAIN WILD-TYPE 283 211
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              105               494 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               34               211 
$`9Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-FP-A8CX 
       60.39         0.36        27.12        20.02        47.05         0.23 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-2H-A9GL TCGA-IC-A6RE TCGA-IG-A50L TCGA-IG-A625 
       20.15        27.35         5.92         7.69         0.53        12.82 
TCGA-JY-A6F8 TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L7-A56G 
      122.10        23.18         3.16         3.32        29.00        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V 
       10.36         5.92        13.41        12.33        13.38        12.59 
TCGA-LN-A49X TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A8I0 TCGA-LN-A9FQ 
       12.62        11.54        12.33         4.47        13.38        12.85 
TCGA-LN-A9FR TCGA-R6-A6L4 TCGA-VR-A8ER TCGA-VR-AA4G TCGA-VR-AA7D TCGA-XP-A8T6 
       12.26        16.31        12.43        18.05         9.17        25.08 
TCGA-Z6-AAPN TCGA-B7-A5TK TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6707 TCGA-BR-7704 
        2.66         9.47        18.35        17.29        19.89        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8289 
       35.84        33.63        18.15        33.21         9.60         2.66 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-A4CQ TCGA-BR-A4J4 
        2.20         6.18        12.79        32.58        34.98         0.53 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5804 
        0.46        20.65        20.42        13.41        13.18        12.10 
TCGA-CD-8535 TCGA-CG-4436 TCGA-CG-4477 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-6528 
       12.82         7.99        30.97        12.66        17.19        15.22 
TCGA-D7-6818 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 
       12.36        14.27        14.76        11.44        15.65         8.38 
TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7735 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
        0.62        21.27         3.48        77.29        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP 
        1.51        28.96         0.76        24.26        22.75         8.98 
TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-R5-A7ZI 
       23.80         3.45         3.39         6.44        63.62        74.53 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PC 
      122.30       115.69        35.61        48.79         5.46        46.26 
TCGA-VQ-A8PP TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z 
       23.41        18.74        32.88        42.64         9.50        55.56 
TCGA-VQ-A922 TCGA-VQ-A94T TCGA-VQ-AA6K 
        9.04        11.24        12.43 

$`9Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-CG-4460 
        4.70        19.99        22.82        35.97         5.16        21.99 
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF 
       22.98        79.07        16.24         9.86        26.93        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L 
        8.71        13.41        83.24        52.57        46.09        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y 
       12.66        12.43        13.15        15.35        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       15.52        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        12.33        13.18         0.13 
TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I 
       33.70        18.18        52.27        46.19        11.24        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        41.23        14.37         3.42         2.10         1.32 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       19.73        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.44         6.61         6.97         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       21.90         9.21        36.16        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59        32.25         8.05         0.56        29.42 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       19.96        15.58         7.40        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        31.96         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        32.52        13.51         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13        13.02        13.15        13.35        11.21        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        25.71        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       13.35        10.26        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 
       26.43        11.24        11.31        20.32        22.29         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
       19.96         7.13         7.99        14.47        72.23        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 
       13.58         0.56         5.52         6.21        63.06        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        18.15        22.32        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       24.30         5.59        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       21.17        14.07        15.68        33.40        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        13.35        19.53         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       17.85         1.87         9.27        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 
       61.22        20.81         1.71        60.85         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.23              0.00 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           122.30            116.38 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            13.38             14.04 
[1] "0.2 - 122.3 (13.4)" "0.0 - 116.4 (14.0)"
[1] "hr=" "1.4"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         2        4       10        4        15        13
  9Q GAIN WILD-TYPE       8       17       37       29        72        74
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           4         19         12          8        8
  9Q GAIN WILD-TYPE        24         76         60         38       41
                   vv
clus                STAGE IVA
  9Q GAIN MUTATED           0
  9Q GAIN WILD-TYPE         4
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 4                17
  STAGE IB                10                37
  STAGE II                 4                29
  STAGE IIA               15                72
  STAGE IIB               13                74
  STAGE III                4                24
  STAGE IIIA              19                76
  STAGE IIIB              12                60
  STAGE IIIC               8                38
  STAGE IV                 8                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9Q GAIN MUTATED      11  22  49  22
  9Q GAIN WILD-TYPE    44 114 234 102
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1              11                44
  T2                 22               114
  T3                 49               234
  T4                 22               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q GAIN MUTATED    37  32  18  17
  9Q GAIN WILD-TYPE 170 155  80  79
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              37               170
  N1              32               155
  N2              18                80
  N3              17                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    95   5
  9Q GAIN WILD-TYPE 429  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     95    5
  9Q GAIN WILD-TYPE  429   34
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              95               429
  1               5                34
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    25  84
  9Q GAIN WILD-TYPE 160 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     25   84
  9Q GAIN WILD-TYPE  160  356
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              25               160
  MALE                84               356
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    71  30
  9Q GAIN WILD-TYPE 374  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     71   30
  9Q GAIN WILD-TYPE  374   89
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               71               374
  YES              30                89
[1] 2 2
[1] FALSE
D18V9, continuous
D18V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED      30                         4
  9Q GAIN WILD-TYPE   104                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           0    59
  9Q GAIN WILD-TYPE                                         1   333
D18V11, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                                  30               104
  BLACK OR AFRICAN AMERICAN                               4                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  59               333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3  73
  9Q GAIN WILD-TYPE   8 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3   73
  9Q GAIN WILD-TYPE    8  331
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              73               331
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    77  54
  10P GAIN WILD-TYPE 277 191
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               131                468 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                54                191 
$`10P GAIN MUTATED`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-CG-4444 TCGA-CG-4460 TCGA-VQ-A94U TCGA-2H-A9GJ 
       15.68        18.28        47.05        21.99        26.93        58.55 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YC TCGA-JY-A6F8 
       13.94        16.24        32.45         7.69        20.12       122.10 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A88V 
       25.22         3.16        26.33        32.61         3.16         2.60 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L7-A6VZ 
        3.02        55.50        12.92        16.47         8.71        10.36 
TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A4A1 TCGA-LN-A4A6 TCGA-LN-A5U6 
       10.45        13.38        13.15        12.59        12.85        12.33 
TCGA-LN-A7HX TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-S8-A6BW 
       12.23         8.02         5.06         6.35        15.78        20.38 
TCGA-V5-AASW TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR 
        9.27         1.55        18.31        52.27        46.19        18.21 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6457 
        2.10         1.32         6.61         4.08        17.29        13.68 
TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.17        40.21         9.21        33.63        39.78        18.15 
TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       28.73         0.69         9.60        29.42         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8682 TCGA-BR-8683 
       15.58         7.40         5.39         9.21        32.58         9.86 
TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.72        32.52        13.51        20.65         1.15        21.44 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A48A 
       13.18        12.76        12.53        12.39        12.30        12.43 
TCGA-CD-A48C TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5730 
       11.61        20.02         4.01        12.00        30.97         4.01 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-8578 
       19.13        20.55        18.84        17.19        12.36        21.14 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 
       16.44        11.31        15.65        19.96         0.62        72.23 
TCGA-FP-7735 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 
        3.48         1.51         5.92        22.32         0.76        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 
       24.20        22.75        25.81        11.77         6.58        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-KB-A93H 
       23.84        21.17        33.40         3.45         3.39        37.64 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
       18.21         6.08        11.05         8.61        16.67       122.30 
TCGA-VQ-A8DU TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX 
        5.46        21.73         7.73        46.26        12.79        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91U TCGA-VQ-A925 TCGA-VQ-AA6J 
       14.33        21.83         1.71         4.54        27.55 

$`10P GAIN WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85         4.31         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       20.02        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK 
        9.86        27.35        25.78        31.27        14.30         7.63 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        5.92         8.94         4.21        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       41.52        47.38        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28        30.25         0.30        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43        15.48        25.12         7.40         3.75 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        2.66        13.48        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37        13.41        83.24        52.57        46.09        10.85 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U 
        5.92        12.66        12.43        13.41        12.33        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        25.25        10.52        12.00        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26        33.11         7.82         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       38.40        53.95         9.30         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        7.00         5.29         3.42        16.44        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX 
       25.81        27.09        22.82        12.43         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        18.18        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08        41.23        14.37         3.42         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        44.94        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       35.84        15.32         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       37.25        14.43        11.44        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        0.56        19.96         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72        25.18        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        0.46        20.42        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 
       13.15        13.35        11.21        12.10        12.59         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH 
       12.82        12.43         6.31        11.31         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05        54.08        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 
       12.03         0.00         9.01        18.97         7.07         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 
        7.99        25.71        12.66        20.91        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       18.21        14.66        20.91        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       22.29         8.38         4.34         7.13         7.99        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
       77.29        63.06        52.21        30.51        26.47        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       18.15        28.96        22.82        21.07        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.68         3.25        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.51        20.25         0.26         2.10        29.00        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       14.07        15.68        36.36        18.81        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A8MW 
        8.52        74.53         4.60         9.24         5.13        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        18.48        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       37.22        30.97        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       13.35        29.59        73.41        39.45        11.70        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        20.81        32.88        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.73        55.56         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        5.72        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        12.43        17.26         0.79 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.62               0.00 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            122.30             116.38 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            13.380             14.055 
[1] "0.6 - 122.3 (13.4)" "0.0 - 116.4 (14.1)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         4        8        7        5        14        22
  10P GAIN WILD-TYPE       6       13       40       28        73        65
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           5         27         13          7       11
  10P GAIN WILD-TYPE        23         68         59         39       38
                    vv
clus                 STAGE IVA
  10P GAIN MUTATED           2
  10P GAIN WILD-TYPE         2
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   4                  6
  STAGE IA                  8                 13
  STAGE IB                  7                 40
  STAGE II                  5                 28
  STAGE IIA                14                 73
  STAGE IIB                22                 65
  STAGE III                 5                 23
  STAGE IIIA               27                 68
  STAGE IIIB               13                 59
  STAGE IIIC                7                 39
  STAGE IV                 11                 38
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10P GAIN MUTATED      18  22  65  25
  10P GAIN WILD-TYPE    37 114 218  99
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1               18                 37
  T2                  22                114
  T3                  65                218
  T4                  25                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P GAIN MUTATED    46  42  22  18
  10P GAIN WILD-TYPE 161 145  76  78
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               46                161
  N1               42                145
  N2               22                 76
  N3               18                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   111  10
  10P GAIN WILD-TYPE 413  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    111   10
  10P GAIN WILD-TYPE  413   29
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0              111                413
  1               10                 29
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    39  97
  10P GAIN WILD-TYPE 146 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     39   97
  10P GAIN WILD-TYPE  146  343
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               39                146
  MALE                 97                343
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   101  24
  10P GAIN WILD-TYPE 344  95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    101   24
  10P GAIN WILD-TYPE  344   95
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO               101                344
  YES               24                 95
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED      34                         4
  10P GAIN WILD-TYPE   100                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           1    82
  10P GAIN WILD-TYPE                                         0   310
D19V11, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                                   34                100
  BLACK OR AFRICAN AMERICAN                                4                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   82                310
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  93
  10P GAIN WILD-TYPE  11 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   93
  10P GAIN WILD-TYPE   11  311
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               93                311
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    53  42
  10Q GAIN WILD-TYPE 301 203
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                95                504 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                42                203 
$`10Q GAIN MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-CG-4444 TCGA-CG-4460 TCGA-VQ-A94U TCGA-2H-A9GJ 
       15.68         4.31        47.05        21.99        26.93        58.55 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-JY-A93E 
       13.94        16.24         7.69         0.79       122.10        25.22 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
       26.33        32.61         3.16         3.02        55.50        12.92 
TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A1 
       16.47        10.36        10.45        13.15        12.59        12.59 
TCGA-LN-A9FQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-VR-A8EQ 
       12.85         5.06         6.35        15.78        20.38        22.82 
TCGA-VR-A8Q7 TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-6456 
       52.27        18.21        19.73         6.61         4.08        17.29 
TCGA-BR-6564 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8077 
       26.10         9.21        33.63        39.78        28.73         0.69 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8682 TCGA-BR-A4J1 
       29.42         2.66        15.58         7.40        32.58         0.72 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 
       32.52        20.65         1.15        13.18        12.76        12.53 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 TCGA-CG-4472 TCGA-CG-4477 TCGA-D7-6519 
       12.39        15.39        20.02        12.00        30.97        20.55 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU 
       18.84        17.19        12.36        18.21        21.14        16.44 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A74A TCGA-F1-6875 TCGA-FP-7735 TCGA-HU-8238 
       11.24        11.31        19.96        72.23         3.48         1.51 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4H4 
       22.32         0.76        24.26        24.20        22.75        23.84 
TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8663 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS 
       21.17         3.45         3.39        18.21         6.08        11.05 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX 
        8.61       122.30        21.73        46.26        12.79        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A928 
       14.33        21.83        20.81         4.54         5.72 

$`10Q GAIN WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       20.02        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK 
        9.86        27.35        25.78        31.27        14.30         7.63 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        5.92         8.94         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ 
       24.03         6.28         3.16        30.25         0.30        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK 
       25.12         7.40         3.75         2.66        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M 
       83.24        52.57        46.09        10.85         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41        12.33        13.38        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.26        33.11         7.82         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.04        38.40        53.95         9.30         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       18.31         8.12        28.11        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 
       14.37         3.42         2.10         1.32         2.66        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 
       15.95        13.87        13.68        19.33        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       35.24        35.84        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       29.56        33.21        37.25        14.43        11.44        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
        9.60        32.25         8.05         0.56        19.96         2.20 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        13.51         0.46        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       12.10        12.59         7.17        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       11.64        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 
       12.03         0.00         9.01        18.97         7.07         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       19.50        17.19        14.66        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ 
       36.43        13.78        14.76        26.43        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       22.29        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 
        7.99        14.47        21.27        11.38        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       26.47         5.92        24.39        18.15        28.96        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GF 
       21.07        24.30         5.59        22.68         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       23.80        14.07        15.68        33.40        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
        2.53         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       19.73        14.04        45.67         8.52        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        9.24         5.13        16.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        18.48        43.36        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        30.97        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       13.35        29.59        73.41        39.45        11.70        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.73        55.56         9.04         2.01        55.43         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.69               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            122.30             116.38 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             16.24              13.53 
[1] "0.7 - 122.3 (16.2)" "0.0 - 116.4 (13.5)"
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         4        7        6        5         7        16
  10Q GAIN WILD-TYPE       6       14       41       28        80        71
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           3         20          9          4        8
  10Q GAIN WILD-TYPE        25         75         63         42       41
                    vv
clus                 STAGE IVA
  10Q GAIN MUTATED           2
  10Q GAIN WILD-TYPE         2
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   4                  6
  STAGE IA                  7                 14
  STAGE IB                  6                 41
  STAGE II                  5                 28
  STAGE IIA                 7                 80
  STAGE IIB                16                 71
  STAGE III                 3                 25
  STAGE IIIA               20                 75
  STAGE IIIB                9                 63
  STAGE IIIC                4                 42
  STAGE IV                  8                 41
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10Q GAIN MUTATED      15  15  50  15
  10Q GAIN WILD-TYPE    40 121 233 109
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1               15                 40
  T2                  15                121
  T3                  50                233
  T4                  15                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED    36  26  20  12
  10Q GAIN WILD-TYPE 171 161  78  84
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               36                171
  N1               26                161
  N2               20                 78
  N3               12                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    81   6
  10Q GAIN WILD-TYPE 443  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     81    6
  10Q GAIN WILD-TYPE  443   33
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               81                443
  1                6                 33
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    29  69
  10Q GAIN WILD-TYPE 156 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     29   69
  10Q GAIN WILD-TYPE  156  371
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               29                156
  MALE                 69                371
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    73  18
  10Q GAIN WILD-TYPE 372 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     73   18
  10Q GAIN WILD-TYPE  372  101
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                73                372
  YES               18                101
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED      21                         3
  10Q GAIN WILD-TYPE   113                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           1    62
  10Q GAIN WILD-TYPE                                         0   330
D20V11, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                                   21                113
  BLACK OR AFRICAN AMERICAN                                3                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   62                330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0  67
  10Q GAIN WILD-TYPE  11 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   67
  10Q GAIN WILD-TYPE   11  337
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               67                337
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    49  43
  11P GAIN WILD-TYPE 305 202
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                92                507 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                43                202 
$`11P GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-FP-A8CX TCGA-2H-A9GN TCGA-2H-A9GO 
       60.39         8.94        24.00         0.23         8.94        16.24 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OU 
       14.50       122.10         3.68        47.93         1.38        29.00 
TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
        2.66         5.49        13.41        52.57        46.09         5.92 
TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.33        12.59        12.46        12.33        13.22         4.47 
TCGA-LN-A8HZ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-RE-A7BO 
       12.33        12.26         7.82         7.59         7.04         7.00 
TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA7I 
        3.42        22.82         8.12        33.70        18.18        15.91 
TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7901 
       19.73        11.01         9.67        13.87        35.24         3.45 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8296 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A4CQ 
       37.25        11.44        15.58        24.79        20.88        34.98 
TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MH 
       12.89        13.51        12.59        12.33        12.30        12.20 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-5722 TCGA-D7-6526 TCGA-D7-8576 TCGA-D7-A6F0 
       20.02        54.08         0.99        17.19        14.66        22.29 
TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-A4G2 TCGA-HU-A4HD 
        7.99        14.07        17.06         5.92        24.30        33.40 
TCGA-IN-A6RJ TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZI 
       12.46        10.62        11.70         5.56        37.64        74.53 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU 
        8.61        16.67       115.69         8.94        35.61         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PX 
       13.02        18.48        43.36        22.19         2.70        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-AA6A 
       14.33        32.88         1.71         9.50         9.73        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F 
       32.94        54.12 

$`11P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        34.85        18.28         4.31         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
        9.86        27.35        26.93        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR 
       58.55         7.63         5.92        13.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       12.16        44.75        68.02        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        3.32         7.17         3.16        58.59         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L7-A56G 
       13.22         7.76        21.37         8.71        83.24        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36        10.45        12.66        12.43        13.41        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.15        15.35        13.25        12.62        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         8.02         5.06        16.31        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       25.81        27.09        12.43         1.55        18.31        28.11 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       52.27        46.19        18.05        11.24         9.17        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        2.66        58.03        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       33.21        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52         0.46        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.35        11.21        12.10        12.76        12.53         7.17 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43         6.31        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        11.77        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       11.38         3.48        19.53        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         1.51        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       28.96        22.32        22.82        21.07         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
        6.44         6.74        12.59         6.51        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         5.13       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       48.79        13.25        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        29.59        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z 
       61.22        18.74        20.81        42.64        60.85        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       43.66        28.41        17.13        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.23               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             122.1              122.3 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            13.315             14.040 
[1] "0.2 - 122.1 (13.3)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         2        4        5        2        12        14
  11P GAIN WILD-TYPE       8       17       42       31        75        73
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           6         12         16          8        8
  11P GAIN WILD-TYPE        22         83         56         38       41
                    vv
clus                 STAGE IVA
  11P GAIN MUTATED           2
  11P GAIN WILD-TYPE         2
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  4                 17
  STAGE IB                  5                 42
  STAGE II                  2                 31
  STAGE IIA                12                 75
  STAGE IIB                14                 73
  STAGE III                 6                 22
  STAGE IIIA               12                 83
  STAGE IIIB               16                 56
  STAGE IIIC                8                 38
  STAGE IV                  8                 41
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11P GAIN MUTATED       8  12  53  19
  11P GAIN WILD-TYPE    47 124 230 105
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                8                 47
  T2                  12                124
  T3                  53                230
  T4                  19                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P GAIN MUTATED    27  27  24  13
  11P GAIN WILD-TYPE 180 160  74  83
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               27                180
  N1               27                160
  N2               24                 74
  N3               13                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    79   7
  11P GAIN WILD-TYPE 445  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     79    7
  11P GAIN WILD-TYPE  445   32
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               79                445
  1                7                 32
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    27  71
  11P GAIN WILD-TYPE 158 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     27   71
  11P GAIN WILD-TYPE  158  369
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               27                158
  MALE                 71                369
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    67  22
  11P GAIN WILD-TYPE 378  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     67   22
  11P GAIN WILD-TYPE  378   97
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                67                378
  YES               22                 97
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED      26                         4
  11P GAIN WILD-TYPE   108                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           1    57
  11P GAIN WILD-TYPE                                         0   335
D21V11, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                                   26                108
  BLACK OR AFRICAN AMERICAN                                4                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   57                335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  56
  11P GAIN WILD-TYPE  10 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   56
  11P GAIN WILD-TYPE   10  348
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               56                348
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    59  37
  11Q GAIN WILD-TYPE 295 208
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                96                503 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                37                208 
$`11Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A88Y TCGA-CG-4444 
       60.39        34.85         8.94        24.00         0.36        47.05 
TCGA-IG-A51D TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-L5-A4OH TCGA-L5-A4OQ 
       17.03        14.50       122.10         3.68        32.61         1.38 
TCGA-L5-A4OU TCGA-L5-A8NN TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49Y TCGA-LN-A4MQ 
       29.00         5.49        13.41         5.92        12.46        12.33 
TCGA-LN-A4MR TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A8W5 
       13.22        12.26         7.82         7.59         7.04        15.78 
TCGA-RE-A7BO TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY TCGA-B7-A5TJ 
        7.00         9.27        22.82         8.12        33.70        11.01 
TCGA-B7-A5TN TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8058 
        9.44         9.67        13.87        35.24         3.45        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8686 
       11.44         0.69        15.58        31.10        27.12        20.88 
TCGA-BR-A4IY TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 
       12.89        12.59        12.33        12.30        12.20        20.02 
TCGA-CG-4438 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5722 TCGA-D7-6526 TCGA-D7-6528 
       54.08        12.00        30.97         0.99        17.19        15.22 
TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 
       14.66        11.24        22.29         7.99        72.23        17.06 
TCGA-HU-8243 TCGA-HU-A4G2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RJ 
        5.92        24.30        23.80        33.40         3.39        12.46 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZI 
        6.74        10.62        11.70         5.56        37.64        74.53 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU 
        8.61        16.67       115.69         8.94        35.61         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PX 
       13.02        18.48        43.36        22.19         2.70        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91Y 
       14.33        21.83        18.74        32.88         1.71         9.73 
TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-ZQ-A9CR 
        4.54        43.66        38.93        32.94        54.12         0.79 

$`11Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        18.28         4.31         4.70        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 
       35.97        27.12         5.16        20.02        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       79.07        16.24         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       26.93        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         7.76        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 
       22.39        12.85        15.52        11.54         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         8.02         5.06        16.31        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
       53.95         9.30         2.89         2.30        12.69        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ 
       27.09        12.43         1.55        18.31        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       19.56         9.47         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       33.63        39.78        18.15        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       29.56        33.21        14.43        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82        12.43         6.31        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.61         6.58        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        10.26        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.31        11.44        20.32 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
       15.68        36.36         3.45        18.81        18.38        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53         6.44        12.59         6.51        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         5.13       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       48.79        13.25        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       13.35        29.59        73.41        39.45        11.70        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       20.81        42.64        60.85         9.50        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.01        55.43         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D 
        2.66        42.54        11.24        18.41        28.41        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.36               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             122.1              122.3 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.64              14.01 
[1] "0.4 - 122.1 (13.6)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.2"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         3        4        6        2         8        19
  11Q GAIN WILD-TYPE       7       17       41       31        79        68
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           4         14         17          7        9
  11Q GAIN WILD-TYPE        24         81         55         39       40
                    vv
clus                 STAGE IVA
  11Q GAIN MUTATED           1
  11Q GAIN WILD-TYPE         3
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  4                 17
  STAGE IB                  6                 41
  STAGE II                  2                 31
  STAGE IIA                 8                 79
  STAGE IIB                19                 68
  STAGE III                 4                 24
  STAGE IIIA               14                 81
  STAGE IIIB               17                 55
  STAGE IIIC                7                 39
  STAGE IV                  9                 40
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11Q GAIN MUTATED       9  16  47  24
  11Q GAIN WILD-TYPE    46 120 236 100
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                9                 46
  T2                  16                120
  T3                  47                236
  T4                  24                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q GAIN MUTATED    27  28  28  11
  11Q GAIN WILD-TYPE 180 159  70  85
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               27                180
  N1               28                159
  N2               28                 70
  N3               11                 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"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    87   5
  11Q GAIN WILD-TYPE 437  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     87    5
  11Q GAIN WILD-TYPE  437   34
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               87                437
  1                5                 34
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    34  68
  11Q GAIN WILD-TYPE 151 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     34   68
  11Q GAIN WILD-TYPE  151  372
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               34                151
  MALE                 68                372
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    69  23
  11Q GAIN WILD-TYPE 376  96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     69   23
  11Q GAIN WILD-TYPE  376   96
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                69                376
  YES               23                 96
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED      22                         4
  11Q GAIN WILD-TYPE   112                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           1    63
  11Q GAIN WILD-TYPE                                         0   329
D22V11, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                                   22                112
  BLACK OR AFRICAN AMERICAN                                4                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   63                329
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  59
  11Q GAIN WILD-TYPE  10 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   59
  11Q GAIN WILD-TYPE   10  345
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               59                345
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    96  49
  12P GAIN WILD-TYPE 258 196
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               145                454 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                196 
$`12P GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NT TCGA-CG-4444 
        4.31        24.00        19.99         0.36        27.12        47.05 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-2H-A9GK TCGA-2H-A9GO 
       21.99        22.98        79.07        16.24         7.63        16.24 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A8O2 
       35.21         2.63        18.64         0.53        23.41         4.67 
TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A8NF TCGA-L5-A8NL 
        0.30        47.93         3.32         4.90         2.66        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        5.49        21.37        10.85        10.36         5.92        10.45 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 
       12.33        13.38        13.15        12.59        13.25        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.76        12.59        12.85        15.52        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.33        25.25        13.18        12.33        13.18         0.13 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW 
        8.02         7.59        38.40        53.95        12.69        20.38 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 
       27.09         1.55        18.31         8.12        28.11        52.27 
TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-A5TK TCGA-BR-6563 TCGA-BR-6566 
       14.37         1.32         2.66         9.47        39.12        32.78 
TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8295 
       12.16        40.21        28.73        33.21        29.59         2.20 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8486 
       31.10         0.26         0.95         3.32         7.36        20.22 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-8526 
        1.48         0.72         1.15        13.41        13.02        12.53 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-6518 
       12.39        12.59         0.99        12.03        12.66        19.13 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A6EX 
       18.54        17.19        11.31        19.50         5.92        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-7735 
       22.29        15.65         8.38        19.96        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HU-8238 TCGA-HU-8249 
       19.53        22.29         5.52         6.21         1.51        28.96 
TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP 
       22.82        24.30         3.25        22.75        25.81         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 
        6.51         6.58        20.25        33.40         3.45         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 
       12.46         6.44         6.74        15.75         2.53        63.62 
TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N6 
       37.64        18.21        74.53         6.08        16.67         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P5 
        5.79        48.79        13.25        18.48        21.73         7.73 
TCGA-VQ-A8PE TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A928 
       22.19        39.45        21.83        20.81        42.64         5.72 
TCGA-VQ-AA6K 
       12.43 

$`12P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         8.94         4.70 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-FP-A8CX TCGA-KB-A93G 
       22.82        35.97         5.16        20.02         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
        9.86        27.35        26.93        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       58.55         5.92        13.94         8.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS 
        7.69        33.27         0.85        20.78        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30        17.03         0.79        12.82         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       16.47        13.55         7.76         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U 
       52.57        46.09        12.66        12.43        13.41        15.35 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.62        12.46        12.49        22.39        11.54        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FP 
       10.52        12.00        12.23        12.03        13.38        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.85        12.26        33.11         7.82         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.04         6.35         9.30        15.78         2.89         2.30 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EY TCGA-VR-A8EZ 
        8.98        25.81        22.82        12.43        33.70        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-3M-AB46 
       25.08        41.23         3.42         2.10        19.73        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10         9.17        25.61        18.05        19.89         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
        2.66        19.96        15.58         7.40         6.18        13.08 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       22.19        17.52        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        34.98        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
        5.13        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 
       12.76        12.59         7.17        12.33        12.30        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02       105.07        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 
       69.04        21.07         7.99        25.71        20.91        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.61        17.85        13.35        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        12.36        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       11.44        20.32         4.34         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 
       14.47        72.23        21.27        14.07        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        5.03        13.58         0.56        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       30.51        26.47         5.92        24.39        18.15        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76         5.59        24.26        22.68        24.20 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77        21.37        29.98         0.10         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       15.68        36.36        18.81        18.38        13.35        19.53 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 
       12.59         6.51        10.62        11.70        13.51         5.56 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       36.95         3.72        19.73        14.04        45.67         8.52 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       35.61        16.87        19.04         0.92         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       43.36        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       46.26        16.31         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N 
       64.57        14.33        73.41        11.70        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       32.88         1.71        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.04         2.01        55.43         4.54         6.58        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.13               0.00 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             79.07             122.30 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             12.85              14.45 
[1] "0.1 - 79.1 (12.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         0        4        8        5        29        20
  12P GAIN WILD-TYPE      10       17       39       28        58        67
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           9         24         15         10       11
  12P GAIN WILD-TYPE        19         71         57         36       38
                    vv
clus                 STAGE IVA
  12P GAIN MUTATED           3
  12P GAIN WILD-TYPE         1
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  4                 17
  STAGE IB                  8                 39
  STAGE II                  5                 28
  STAGE IIA                29                 58
  STAGE IIB                20                 67
  STAGE III                 9                 19
  STAGE IIIA               24                 71
  STAGE IIIB               15                 57
  STAGE IIIC               10                 36
  STAGE IV                 11                 38
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12P GAIN MUTATED      12  29  83  19
  12P GAIN WILD-TYPE    43 107 200 105
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               12                 43
  T2                  29                107
  T3                  83                200
  T4                  19                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P GAIN MUTATED    51  43  28  19
  12P GAIN WILD-TYPE 156 144  70  77
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               51                156
  N1               43                144
  N2               28                 70
  N3               19                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   120  12
  12P GAIN WILD-TYPE 404  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    120   12
  12P GAIN WILD-TYPE  404   27
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0              120                404
  1               12                 27
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    35 114
  12P GAIN WILD-TYPE 150 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     35  114
  12P GAIN WILD-TYPE  150  326
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               35                150
  MALE                114                326
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   101  34
  12P GAIN WILD-TYPE 344  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    101   34
  12P GAIN WILD-TYPE  344   85
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO               101                344
  YES               34                 85
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED      43                         5
  12P GAIN WILD-TYPE    91                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           0    87
  12P GAIN WILD-TYPE                                         1   305
D23V11, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                                   43                 91
  BLACK OR AFRICAN AMERICAN                                5                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   87                305
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     4 102
  12P GAIN WILD-TYPE   7 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4  102
  12P GAIN WILD-TYPE    7  302
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO              102                302
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    74  40
  12Q GAIN WILD-TYPE 280 205
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               114                485 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                40                205 
$`12Q GAIN MUTATED`
TCGA-L5-A4OE TCGA-L5-A88Y TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 
       24.00         0.36        27.12        47.05        21.99        79.07 
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A4OM 
        7.63        16.24         2.63         0.53         4.67        47.93 
TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L7-A6VZ 
        3.32         4.90        13.22         5.49        52.57        10.36 
TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A6 TCGA-LN-A4A8 
       10.45        12.59        13.25        12.59        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A8HZ 
       11.54        12.33         4.47        12.33        25.25        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A8WG TCGA-VR-A8EP 
       13.18         0.13         7.59        38.40        12.69        27.09 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TK 
       18.31        28.11        52.27         2.66        19.73         9.47 
TCGA-BR-4267 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-7723 TCGA-BR-7959 
        6.18        39.12        32.78        12.16        28.73        33.21 
TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8381 
       29.59         2.20         0.26         0.95         3.32         7.36 
TCGA-BR-8589 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5798 TCGA-CD-5799 
       27.12         1.48         0.72         0.53        13.41        13.02 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4472 
       12.53        12.39        12.82        12.30        12.43        12.00 
TCGA-CG-5722 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 
        0.99        12.66        19.13        18.54        17.19        10.26 
TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A747 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-7916 
       19.50         5.92         8.38        19.96        11.38        14.07 
TCGA-FP-7998 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
       22.29         5.52         6.21         1.51        28.96        22.82 
TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       24.30         3.25        22.75         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ 
       20.25        23.84        33.40         3.45         3.39        12.46 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7C1 
       15.75         2.53        63.62        74.53         6.08        16.67 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
        8.94         5.79        48.79         7.73        22.19         2.70 
TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A928 
       14.33        21.83        20.81        42.64         9.50         5.72 

$`12Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        19.99        22.82        35.97         5.16        20.02 
TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       22.98        16.24         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL 
       26.93        25.78        31.27        14.30        58.55         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85        20.78        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       26.33        32.61        21.01        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        46.09        10.85 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
        5.92        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.59        22.39        13.22        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.03        13.18        13.38        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        33.70        18.18        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         1.32        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       17.29        13.68        19.33        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       33.63        39.78        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       29.56        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 
       15.58         7.40         6.18        31.10        13.08        22.19 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
       17.52        26.33         4.31        14.04        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        34.98        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.59         7.17        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C 
       15.39        12.07        12.43         6.31        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       25.71        20.91        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        16.80        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       22.29        15.65         4.34         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
       14.47        72.23        21.27         3.48        19.53        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7133 
       59.54         5.03        13.58         0.56        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         5.92        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.32        21.07         0.76         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
       14.07        15.68        36.36        18.81        18.38        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       11.70        13.51         5.56        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A804 
       19.73        14.04        45.67        18.21         8.52         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87        19.04         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       29.59        64.57        73.41        39.45        11.70        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       18.74        32.88         1.71        60.85         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.04         2.01        55.43         4.54         6.58        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.13               0.00 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             79.07             122.30 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             12.56              14.50 
[1] "0.1 - 79.1 (12.6)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0        3        4        6        20        14
  12Q GAIN WILD-TYPE      10       18       43       27        67        73
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           6         19         15          7       12
  12Q GAIN WILD-TYPE        22         76         57         39       37
                    vv
clus                 STAGE IVA
  12Q GAIN MUTATED           2
  12Q GAIN WILD-TYPE         2
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  3                 18
  STAGE IB                  4                 43
  STAGE II                  6                 27
  STAGE IIA                20                 67
  STAGE IIB                14                 73
  STAGE III                 6                 22
  STAGE IIIA               19                 76
  STAGE IIIB               15                 57
  STAGE IIIC                7                 39
  STAGE IV                 12                 37
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12Q GAIN MUTATED       8  21  65  19
  12Q GAIN WILD-TYPE    47 115 218 105
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                8                 47
  T2                  21                115
  T3                  65                218
  T4                  19                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q GAIN MUTATED    34  35  27  15
  12Q GAIN WILD-TYPE 173 152  71  81
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               34                173
  N1               35                152
  N2               27                 71
  N3               15                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    94  11
  12Q GAIN WILD-TYPE 430  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     94   11
  12Q GAIN WILD-TYPE  430   28
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               94                430
  1               11                 28
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    28  88
  12Q GAIN WILD-TYPE 157 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     28   88
  12Q GAIN WILD-TYPE  157  352
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               28                157
  MALE                 88                352
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    82  22
  12Q GAIN WILD-TYPE 363  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     82   22
  12Q GAIN WILD-TYPE  363   97
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                82                363
  YES               22                 97
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED      39                         1
  12Q GAIN WILD-TYPE    95                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           0    62
  12Q GAIN WILD-TYPE                                         1   330
D24V11, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                                   39                 95
  BLACK OR AFRICAN AMERICAN                                1                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   62                330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     3  80
  12Q GAIN WILD-TYPE   8 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   80
  12Q GAIN WILD-TYPE    8  324
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               80                324
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED   113  74
  13Q GAIN WILD-TYPE 241 171
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               187                412 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                74                171 
$`13Q GAIN MUTATED`
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NT 
       18.28         8.94         4.70        19.99         0.36        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-MX-A663 TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL 
       20.02        47.05         9.86        31.27        14.30         5.92 
TCGA-2H-A9GM TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH 
       13.94         0.79        14.50       122.10         3.68        47.38 
TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OP TCGA-L5-A4OQ 
       23.18        31.56         3.16        30.25         7.17         1.38 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-LN-A4MQ 
        7.13         2.60         3.02         2.66        12.92        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6L4 
       25.25        12.00        13.18        12.85         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-A7RC 
        7.04        38.40         9.30        15.78         5.29         3.42 
TCGA-V5-AASW TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-ZR-A9CJ TCGA-B7-5818 
        9.27        46.19        18.21        25.08        19.73        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 
       11.01         9.44         4.64         9.67         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 
       15.95        39.12         9.17        32.78        25.61        40.21 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8078 
        9.21        35.24        18.15        28.73         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8483 
        9.60        29.42        13.08        14.79        25.05         5.39 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        9.21        12.79        24.79        32.58        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J8 
       10.68        13.87         0.72        14.17        28.34        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5799 
        0.46        20.65        20.42         1.15         5.13        13.02 
TCGA-CD-5800 TCGA-CD-8529 TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
       13.15        12.30        12.82        12.43         6.58        12.20 
TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4469 TCGA-CG-4472 
       20.02        15.95         7.99        54.08         7.07        12.00 
TCGA-CG-5719 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        1.02         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       19.13        18.54        17.85        17.19        10.26        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-A4YT TCGA-D7-A4Z0 
       12.36        11.31        19.50        17.19        14.27        14.76 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-EQ-5647 TCGA-EQ-8122 
       11.24        22.29        15.65         8.38         0.62         7.99 
TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-A4BF TCGA-HF-7134 TCGA-HU-8245 TCGA-HU-8249 
       72.23        19.53         5.52        52.21        18.15        28.96 
TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT 
       22.82        24.26        22.68        22.75        25.81         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD 
        6.58         0.26        29.00        23.84        23.80        33.40 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
       18.38        13.35         6.44        11.70         5.56        37.64 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A8MV 
       14.04        45.67        18.21         8.52         8.61       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
       37.91       115.69        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        21.73        37.41 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PY 
       22.19         2.70        17.85        23.41        13.35        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       73.41        39.45        20.81        32.88         1.71        42.64 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6J 
        9.04        21.04        42.54        11.24        32.94        27.55 
TCGA-VQ-AA6K 
       12.43 

$`13Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A88T 
       15.68        60.39        34.85         4.31        24.00        22.82 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       35.97         5.16        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GJ 
        0.23        20.15        27.35        26.93        25.78        58.55 
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        7.63         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96        14.86         4.67        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       68.02        41.52        21.70        25.22        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         3.16        58.59         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NI 
       15.48        25.12         7.40         3.75        55.50        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        10.52        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN 
       13.38         0.13        12.03        12.26        33.11         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.59         5.06         6.35        53.95         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
       12.69         7.00        20.38        16.44        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       11.24         9.17        15.91        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI 
        2.10         1.32         2.66        58.03        26.70        19.56 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         6.61         6.97         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 
        4.08         4.08         9.34         6.18        34.68        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-6707 
       17.29        13.68        19.33        26.10        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 
       36.16        35.84        33.63        39.78        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 
       11.80        31.27         7.36         3.72        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       26.73        31.96         9.86        34.13         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.53         0.66        32.52        21.44        16.14        13.41 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.43         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.61        11.77        12.62         3.02        27.02         1.02 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       28.96        65.10        21.07        20.91        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 
       18.61        13.35        15.22        12.79        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       16.80        18.21        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        36.43        13.78        26.43        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 
       20.32         4.34        19.96         7.13        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         0.56         6.21        77.29        63.06 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       30.51        26.47         1.51         5.92        24.39        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC 
       21.07         0.76        24.30         5.59        24.20         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         0.10        20.25 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        2.10        12.95        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
        3.45        18.81         3.39        12.46        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        10.62        15.75        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR 
       63.62        36.95         3.72        19.73        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        4.60         9.24        11.05         5.13        16.67        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 
      116.38        71.38        16.87        19.04         0.92        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       43.36        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.50        12.79         1.87         9.27 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       15.65        29.59        64.57        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 
       18.74        60.85         9.50         9.73        55.56         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        66.81         2.66 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        17.26         0.79 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.26               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            122.30             116.38 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             14.27              13.63 
[1] "0.3 - 122.3 (14.3)" "0.0 - 116.4 (13.6)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         5        5       10       11        20        28
  13Q GAIN WILD-TYPE       5       16       37       22        67        59
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           6         32         24         14       20
  13Q GAIN WILD-TYPE        22         63         48         32       29
                    vv
clus                 STAGE IVA
  13Q GAIN MUTATED           2
  13Q GAIN WILD-TYPE         2
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   5                  5
  STAGE IA                  5                 16
  STAGE IB                 10                 37
  STAGE II                 11                 22
  STAGE IIA                20                 67
  STAGE IIB                28                 59
  STAGE III                 6                 22
  STAGE IIIA               32                 63
  STAGE IIIB               24                 48
  STAGE IIIC               14                 32
  STAGE IV                 20                 29
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  13Q GAIN MUTATED      18  44  83  40
  13Q GAIN WILD-TYPE    37  92 200  84
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1               18                 37
  T2                  44                 92
  T3                  83                200
  T4                  40                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q GAIN MUTATED    54  56  37  34
  13Q GAIN WILD-TYPE 153 131  61  62
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               54                153
  N1               56                131
  N2               37                 61
  N3               34                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   163  13
  13Q GAIN WILD-TYPE 361  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    163   13
  13Q GAIN WILD-TYPE  361   26
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0              163                361
  1               13                 26
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    53 144
  13Q GAIN WILD-TYPE 132 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     53  144
  13Q GAIN WILD-TYPE  132  296
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               53                132
  MALE                144                296
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   144  33
  13Q GAIN WILD-TYPE 301  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    144   33
  13Q GAIN WILD-TYPE  301   86
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO               144                301
  YES               33                 86
[1] 2 2
[1] FALSE
D25V9, continuous
D25V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED      37                         8
  13Q GAIN WILD-TYPE    97                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           1   122
  13Q GAIN WILD-TYPE                                         0   270
D25V11, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                                   37                 97
  BLACK OR AFRICAN AMERICAN                                8                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  122                270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4 127
  13Q GAIN WILD-TYPE   7 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4  127
  13Q GAIN WILD-TYPE    7  277
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO              127                277
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    43  31
  14Q GAIN WILD-TYPE 311 214
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                74                525 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                31                214 
$`14Q GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A8NG TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-2H-A9GL 
        4.31        35.97        20.02        47.05        21.99         5.92 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6FG 
        0.85        20.78        18.64         9.96        12.16        41.52 
TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OX TCGA-L5-A8NN TCGA-L5-A8NQ 
       23.18         3.16        30.25         7.43         5.49        21.37 
TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       13.41         5.92        13.15        15.35        12.59        12.62 
TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.59        12.59        11.54        13.22        12.33        25.25 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.03        13.18        12.33         0.13        12.03        12.26 
TCGA-R6-A6DN TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-AASX TCGA-VR-A8EW TCGA-VR-AA4D 
        8.02        53.95        20.38         8.98         8.12        46.19 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        25.08         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-BR-4187 TCGA-BR-6705 TCGA-BR-8060 TCGA-BR-8295 
        1.32        19.73         4.64        25.61        11.44         2.20 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-CD-A48A TCGA-D7-6518 TCGA-D7-A6F2 TCGA-EQ-5647 
       13.51        20.42        12.43        19.13        15.65         0.62 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-IN-A6RI TCGA-IN-A7NR TCGA-IN-A7NT TCGA-R5-A7O7 
        5.52         5.92        18.38         6.51        10.62        45.67 
TCGA-R5-A7ZF TCGA-RD-A7BS TCGA-VQ-A8PE TCGA-VQ-A91V TCGA-VQ-A925 TCGA-VQ-A94R 
        8.52        11.05        22.19        42.64         4.54        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6I 
       43.66        16.14 

$`14Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       27.35        26.93        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
        7.69        33.27        35.21         2.63        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        14.50       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
        3.68        47.38        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        6.28         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.13        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR 
       13.48        16.47        13.55        13.22         7.76         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       83.24        52.57        46.09        10.85        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W 
       12.66        12.43        13.41        12.33        13.38        13.25 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.49        12.76        22.39        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I0 
       12.33         4.47        10.52        12.00        12.23        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
       13.18        12.85        33.11         7.82         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       52.27        18.05        18.21        41.23        14.37         2.66 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         6.97         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52         0.46        20.65         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       20.91        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM 
       17.06        59.54         5.03        13.58         0.56         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       63.62        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT 
       18.21        74.53         6.08         4.60         9.24         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       20.81        32.88         1.71        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       55.56         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
       66.81        21.04         2.66        11.24        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       38.93        32.94        17.13        54.12        26.04        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.13               0.00 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             53.95             122.30 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             12.59              14.30 
[1] "0.1 - 54.0 (12.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         2        1        3        0        16        13
  14Q GAIN WILD-TYPE       8       20       44       33        71        74
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           7         11          6          5        6
  14Q GAIN WILD-TYPE        21         84         66         41       43
                    vv
clus                 STAGE IVA
  14Q GAIN MUTATED           0
  14Q GAIN WILD-TYPE         4
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  1                 20
  STAGE IB                  3                 44
  STAGE II                  0                 33
  STAGE IIA                16                 71
  STAGE IIB                13                 74
  STAGE III                 7                 21
  STAGE IIIA               11                 84
  STAGE IIIB                6                 66
  STAGE IIIC                5                 41
  STAGE IV                  6                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  14Q GAIN MUTATED       4  21  35  11
  14Q GAIN WILD-TYPE    51 115 248 113
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                4                 51
  T2                  21                115
  T3                  35                248
  T4                  11                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q GAIN MUTATED    29  21   8  13
  14Q GAIN WILD-TYPE 178 166  90  83
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               29                178
  N1               21                166
  N2                8                 90
  N3               13                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    62   6
  14Q GAIN WILD-TYPE 462  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     62    6
  14Q GAIN WILD-TYPE  462   33
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               62                462
  1                6                 33
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    14  62
  14Q GAIN WILD-TYPE 171 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     14   62
  14Q GAIN WILD-TYPE  171  378
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               14                171
  MALE                 62                378
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    52  21
  14Q GAIN WILD-TYPE 393  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     52   21
  14Q GAIN WILD-TYPE  393   98
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                52                393
  YES               21                 98
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED      22                         2
  14Q GAIN WILD-TYPE   112                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           0    47
  14Q GAIN WILD-TYPE                                         1   345
D26V11, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                                   22                112
  BLACK OR AFRICAN AMERICAN                                2                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   47                345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  50
  14Q GAIN WILD-TYPE   9 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   50
  14Q GAIN WILD-TYPE    9  354
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               50                354
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    31  33
  15Q GAIN WILD-TYPE 323 212
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                64                535 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                212 
$`15Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-CG-5727 TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IG-A50L 
       60.39         0.36        79.07         7.63         8.94         0.53 
TCGA-JY-A6F8 TCGA-L5-A43C TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
      122.10         3.16         3.16         7.13        15.48         2.60 
TCGA-L5-A8NJ TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4MR 
       16.47        46.09        10.85        10.45        13.38        13.22 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.00        12.23        12.33        33.11         7.82         7.59 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-AA7D 
        7.04         6.35        27.09        22.82         1.55         9.17 
TCGA-XP-A8T7 TCGA-BR-4183 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7959 TCGA-BR-8683 
       41.23         6.61        12.16         9.21        33.21         9.86 
TCGA-BR-8687 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-A486 TCGA-CG-4477 TCGA-D7-6520 
        8.22         1.15        13.02         6.31        30.97        18.84 
TCGA-D7-6525 TCGA-D7-6815 TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 
       13.35        15.98         0.62        72.23        11.38        17.06 
TCGA-HU-A4GH TCGA-IN-7808 TCGA-IN-8663 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE 
       11.77         3.45         3.39        63.62        37.64        18.21 
TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PC 
        6.08         8.61       122.30        13.02        18.48        46.26 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A925 
       12.79         2.70        17.85         4.54 

$`15Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        21.99        22.98        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       20.15         9.86        27.35        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30        58.55         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        4.90        29.00         7.43        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        3.02        55.50         2.66        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       22.39        12.85        15.52        11.54        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       12.33        25.25        10.52        12.03        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN 
       13.18         0.13        12.03        12.85        12.26         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        16.31        38.40        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        18.05        11.24        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       19.73        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       32.58        20.88        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       32.52        13.51         0.46        20.65        20.42        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       16.14         5.13        13.41        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82        12.43        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       20.55        18.54        18.61        17.85        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        14.47        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       21.17        14.07        15.68        33.40        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       45.67         8.52        74.53         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 
        5.79         0.92        48.79         5.46        13.25        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO 
       34.29        16.31        22.19         2.50         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.73        55.56         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        5.72        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.36               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            122.30             116.38 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             12.08              14.33 
[1] "0.4 - 122.3 (12.1)" "0.0 - 116.4 (14.3)"
[1] "hr=" "1.4"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         2        4        4        3        11         4
  15Q GAIN WILD-TYPE       8       17       43       30        76        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           7          9          8          3        5
  15Q GAIN WILD-TYPE        21         86         64         43       44
                    vv
clus                 STAGE IVA
  15Q GAIN MUTATED           0
  15Q GAIN WILD-TYPE         4
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  4                 17
  STAGE IB                  4                 43
  STAGE II                  3                 30
  STAGE IIA                11                 76
  STAGE IIB                 4                 83
  STAGE III                 7                 21
  STAGE IIIA                9                 86
  STAGE IIIB                8                 64
  STAGE IIIC                3                 43
  STAGE IV                  5                 44
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  15Q GAIN MUTATED       7  16  30   9
  15Q GAIN WILD-TYPE    48 120 253 115
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1                7                 48
  T2                  16                120
  T3                  30                253
  T4                   9                115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q GAIN MUTATED    22  15  15   9
  15Q GAIN WILD-TYPE 185 172  83  87
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               22                185
  N1               15                172
  N2               15                 83
  N3                9                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    52   5
  15Q GAIN WILD-TYPE 472  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     52    5
  15Q GAIN WILD-TYPE  472   34
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               52                472
  1                5                 34
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    14  53
  15Q GAIN WILD-TYPE 171 387
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     14   53
  15Q GAIN WILD-TYPE  171  387
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               14                171
  MALE                 53                387
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    49  13
  15Q GAIN WILD-TYPE 396 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     49   13
  15Q GAIN WILD-TYPE  396  106
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                49                396
  YES               13                106
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED      14                         5
  15Q GAIN WILD-TYPE   120                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           1    36
  15Q GAIN WILD-TYPE                                         0   356
D27V11, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                                   14                120
  BLACK OR AFRICAN AMERICAN                                5                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   36                356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  36
  15Q GAIN WILD-TYPE  10 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   36
  15Q GAIN WILD-TYPE   10  368
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               36                368
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    58  38
  16P GAIN WILD-TYPE 296 207
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                96                503 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                207 
$`16P GAIN MUTATED`
TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX TCGA-2H-A9GJ 
       27.12        47.05        21.99        22.98         0.23        58.55 
TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-L5-A43H 
        0.85         0.53         0.79         4.67        14.50         0.30 
TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NQ 
        3.32        29.00        15.48        55.50         2.66        21.37 
TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A1 
       13.41        10.36         5.92        13.15        13.25        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 
       12.76        12.59        12.85        11.54        13.22        12.33 
TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6KZ TCGA-R6-A6XG 
       12.03        13.18         0.13        12.85         5.06        38.40 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8EW 
       15.78         2.89        20.38        15.35        12.43         8.12 
TCGA-VR-A8EX TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN 
       28.11        14.37         3.42        19.73        11.01         9.44 
TCGA-BR-4187 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-8080 TCGA-BR-8484 
        4.64         9.67        17.29         9.17         9.60        25.18 
TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-CD-5801 
       20.22         7.53        28.34        13.51        20.65        13.18 
TCGA-CD-5804 TCGA-CD-8528 TCGA-CD-8529 TCGA-CG-4438 TCGA-CG-4462 TCGA-CG-4472 
       12.10        12.33        12.30        54.08         0.00        12.00 
TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6817 
        1.02         0.99         4.01        18.54        17.19        12.79 
TCGA-D7-6818 TCGA-D7-8576 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       12.36        14.66         3.48        14.07        22.29        17.06 
TCGA-FP-8631 TCGA-HU-8249 TCGA-HU-A4GP TCGA-HU-A4GY TCGA-IN-8663 TCGA-IN-A6RL 
        0.56        28.96         8.98         0.26         3.39        13.35 
TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-R5-A7ZE TCGA-RD-A7BT 
        6.44        10.62        11.70         2.53        18.21         8.61 
TCGA-VQ-A8PS TCGA-VQ-A925 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6K 
       13.35         4.54        32.94        54.12        16.14        12.43 

$`16P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
        5.16        20.02        79.07        16.24        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK 
       27.35        26.93        25.78        31.27        14.30         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        33.27        35.21        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
       18.64         3.88         9.30        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        3.16        58.59         4.90         7.13         7.43         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         7.40         3.75         3.02        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76         5.49         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        46.09        10.85        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.38        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.62        12.46        12.49        22.39        15.52        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.33        13.38        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59        16.31         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        9.30         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55        18.31        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 
       41.23         2.10         1.32         2.66        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 
       11.70        19.56         9.47         6.61         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
       14.79         7.36        25.05         3.72         5.39         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       20.88         8.22        10.68        34.13        13.87         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
        0.72        14.17         0.53         0.66        32.52         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.02        13.15        13.35        11.21        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.53         7.17        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 
       13.35        10.26        15.22        15.98        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7829 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM 
       19.53        59.54         5.03        13.58         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        18.15        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58        20.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36         3.45        18.81        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53         6.74        12.59         6.51        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        27.55        17.26         0.79 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               0.0                0.1 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             58.55             122.30 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             12.59              15.02 
[1] "0.0 - 58.5 (12.6)"  "0.1 - 122.3 (15.0)"
[1] "hr=" "1.3"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         1        2        5        1        14        16
  16P GAIN WILD-TYPE       9       19       42       32        73        71
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           6         18          8          9       10
  16P GAIN WILD-TYPE        22         77         64         37       39
                    vv
clus                 STAGE IVA
  16P GAIN MUTATED           3
  16P GAIN WILD-TYPE         1
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  2                 19
  STAGE IB                  5                 42
  STAGE II                  1                 32
  STAGE IIA                14                 73
  STAGE IIB                16                 71
  STAGE III                 6                 22
  STAGE IIIA               18                 77
  STAGE IIIB                8                 64
  STAGE IIIC                9                 37
  STAGE IV                 10                 39
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16P GAIN MUTATED       7  19  47  22
  16P GAIN WILD-TYPE    48 117 236 102
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                7                 48
  T2                  19                117
  T3                  47                236
  T4                  22                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P GAIN MUTATED    32  28  15  17
  16P GAIN WILD-TYPE 175 159  83  79
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               32                175
  N1               28                159
  N2               15                 83
  N3               17                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    75   9
  16P GAIN WILD-TYPE 449  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     75    9
  16P GAIN WILD-TYPE  449   30
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               75                449
  1                9                 30
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    21  79
  16P GAIN WILD-TYPE 164 361
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     21   79
  16P GAIN WILD-TYPE  164  361
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               21                164
  MALE                 79                361
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    63  23
  16P GAIN WILD-TYPE 382  96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     63   23
  16P GAIN WILD-TYPE  382   96
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                63                382
  YES               23                 96
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED      29                         3
  16P GAIN WILD-TYPE   105                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           1    54
  16P GAIN WILD-TYPE                                         0   338
D28V11, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                                   29                105
  BLACK OR AFRICAN AMERICAN                                3                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   54                338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     2  68
  16P GAIN WILD-TYPE   9 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   68
  16P GAIN WILD-TYPE    9  336
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               68                336
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    46  36
  16Q GAIN WILD-TYPE 308 209
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                82                517 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                36                209 
$`16Q GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A8NT TCGA-CG-4460 TCGA-FP-A8CX TCGA-2H-A9GM TCGA-IG-A3Y9 
        4.31        27.12        21.99         0.23        13.94         0.85 
TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S 
        0.79         4.67         0.30         3.32        29.00        15.48 
TCGA-L5-A8NF TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49R TCGA-LN-A49S 
        2.66        21.37        13.41        52.57        13.38        13.15 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 
       12.59        12.76        12.59        12.85        11.54        12.33 
TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6XG TCGA-R6-A8W5 
       12.03        13.18         0.13        12.85        38.40        15.78 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX 
       20.38         3.42        15.35        12.43         8.12        28.11 
TCGA-VR-AA7B TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-A5TJ 
       11.24        14.37         3.42         2.10        19.73        11.01 
TCGA-BR-4187 TCGA-BR-4257 TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J5 
        4.64         9.67        20.22         7.53         1.48        28.34 
TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8529 TCGA-CG-4438 TCGA-CG-4462 
       13.51        13.18        12.33        12.30        54.08         0.00 
TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-6521 TCGA-D7-6818 
       12.00         1.02         0.99         4.01        18.54        12.36 
TCGA-D7-8576 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       14.66         7.99         3.48        14.07        22.29        17.06 
TCGA-FP-8631 TCGA-HU-8249 TCGA-HU-A4GP TCGA-IN-8663 TCGA-IN-A6RP TCGA-IN-A6RR 
        0.56        28.96         8.98         3.39         6.44         6.74 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-VQ-A8DV TCGA-VQ-A8PS 
       10.62        11.70        18.21         8.61        13.25        13.35 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6K 
       32.94        54.12        16.14        12.43 

$`16Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        35.97         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       20.02        47.05        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
        9.86        27.35        26.93        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63         5.92         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        33.27        35.21        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW 
       13.22         7.76         5.49         8.71        83.24        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        12.33        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.46        12.49        22.39        15.52        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.33        13.38        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        5.29        16.44         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       22.82         1.55        18.31        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        18.05         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       41.23         1.32         2.66        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 
       19.56         9.47         9.44         6.61         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18         9.21         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       10.68        34.13        13.87         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
        7.17        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
        4.01        14.01        29.98        19.07        12.03         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       18.97         7.07        30.97         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        12.79        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7829 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM 
       19.53        59.54         5.03        13.58         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        18.15        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
       12.46        13.35        19.53        12.59         6.51        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 
       28.41        38.93        17.13        26.04        27.55        17.26 
TCGA-ZQ-A9CR 
        0.79 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               0.0                0.1 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             54.12             122.30 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             12.43              15.02 
[1] "0.0 - 54.1 (12.4)"  "0.1 - 122.3 (15.0)"
[1] "hr=" "1.5"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0        2        6        1        12        13
  16Q GAIN WILD-TYPE      10       19       41       32        75        74
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           6         12          7          8       11
  16Q GAIN WILD-TYPE        22         83         65         38       38
                    vv
clus                 STAGE IVA
  16Q GAIN MUTATED           3
  16Q GAIN WILD-TYPE         1
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  2                 19
  STAGE IB                  6                 41
  STAGE II                  1                 32
  STAGE IIA                12                 75
  STAGE IIB                13                 74
  STAGE III                 6                 22
  STAGE IIIA               12                 83
  STAGE IIIB                7                 65
  STAGE IIIC                8                 38
  STAGE IV                 11                 38
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16Q GAIN MUTATED       7  15  43  17
  16Q GAIN WILD-TYPE    48 121 240 107
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                7                 48
  T2                  15                121
  T3                  43                240
  T4                  17                107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16Q GAIN MUTATED    30  24  11  16
  16Q GAIN WILD-TYPE 177 163  87  80
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               30                177
  N1               24                163
  N2               11                 87
  N3               16                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    61  10
  16Q GAIN WILD-TYPE 463  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     61   10
  16Q GAIN WILD-TYPE  463   29
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               61                463
  1               10                 29
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    18  68
  16Q GAIN WILD-TYPE 167 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     18   68
  16Q GAIN WILD-TYPE  167  372
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               18                167
  MALE                 68                372
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    52  22
  16Q GAIN WILD-TYPE 393  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     52   22
  16Q GAIN WILD-TYPE  393   97
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                52                393
  YES               22                 97
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED      23                         4
  16Q GAIN WILD-TYPE   111                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           1    47
  16Q GAIN WILD-TYPE                                         0   345
D29V11, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                                   23                111
  BLACK OR AFRICAN AMERICAN                                4                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   47                345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2  55
  16Q GAIN WILD-TYPE   9 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   55
  16Q GAIN WILD-TYPE    9  349
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               55                349
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    32  27
  17P GAIN WILD-TYPE 322 218
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                59                540 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                27                218 
$`17P GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A8NG TCGA-CG-4460 TCGA-CG-4475 
       60.39        18.28         4.31        35.97        21.99        22.98 
TCGA-EQ-A4SO TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-JY-A93C 
       16.24         7.69        35.21         0.53        17.03        23.18 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A88Z TCGA-L5-A8NE 
       25.22         0.30        18.35         1.38         7.40        55.50 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A7HW 
       13.41        13.38        12.59        12.49        12.59        12.00 
TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-V5-A7RC TCGA-VR-A8ET 
       13.18        12.26         8.02         5.06         3.42         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-BR-8059 
       18.31        33.70        46.19        15.91         2.10        14.43 
TCGA-BR-8060 TCGA-BR-8686 TCGA-BR-A4QI TCGA-CD-A48A TCGA-CG-4455 TCGA-CG-5722 
       11.44        20.88        21.44        12.43        12.03         0.99 
TCGA-CG-5724 TCGA-D7-6817 TCGA-D7-8573 TCGA-D7-A6EY TCGA-EQ-5647 TCGA-FP-7829 
       12.03        12.79        19.50        11.44         0.62        19.53 
TCGA-HJ-7597 TCGA-HU-A4GF TCGA-HU-A4HD TCGA-MX-A666 TCGA-R5-A7ZR TCGA-VQ-A91Z 
       26.47        25.81        33.40        14.04         6.08        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
        9.04         2.01         4.54        21.04        42.54 

$`17P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        34.85         8.94        24.00         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 
       22.82         0.36        27.12         5.16        20.02        47.05 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07         0.23        20.15         9.86        27.35        26.93 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
        3.68        41.52        47.38        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         3.32         7.17         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S 
        5.92        10.45        12.66        12.43        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       15.35        13.25        12.62        12.46        12.59        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        25.25        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.38         0.13        12.03        12.85 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         7.82         7.59        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       29.56        33.21        37.25         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
       54.08         4.01        14.01        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 
       36.00         1.02         0.99         6.02       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
        2.53         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       19.73        45.67        18.21         8.52        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 
        1.71        42.64        60.85         9.50         9.73        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58         5.72        66.81         2.66        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               0.3                0.0 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             60.39             122.30 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            13.380             14.025 
[1] "0.3 - 60.4 (13.4)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.2"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         1        0        1        1        15        10
  17P GAIN WILD-TYPE       9       21       46       32        72        77
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           7         10          4          1        6
  17P GAIN WILD-TYPE        21         85         68         45       43
                    vv
clus                 STAGE IVA
  17P GAIN MUTATED           0
  17P GAIN WILD-TYPE         4
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 21
  STAGE IB                  1                 46
  STAGE II                  1                 32
  STAGE IIA                15                 72
  STAGE IIB                10                 77
  STAGE III                 7                 21
  STAGE IIIA               10                 85
  STAGE IIIB                4                 68
  STAGE IIIC                1                 45
  STAGE IV                  6                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17P GAIN MUTATED       7  12  30   9
  17P GAIN WILD-TYPE    48 124 253 115
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1                7                 48
  T2                  12                124
  T3                  30                253
  T4                   9                115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P GAIN MUTATED    17  26   7   5
  17P GAIN WILD-TYPE 190 161  91  91
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               17                190
  N1               26                161
  N2                7                 91
  N3                5                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    45   5
  17P GAIN WILD-TYPE 479  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     45    5
  17P GAIN WILD-TYPE  479   34
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               45                479
  1                5                 34
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    12  49
  17P GAIN WILD-TYPE 173 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     12   49
  17P GAIN WILD-TYPE  173  391
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               12                173
  MALE                 49                391
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    38  16
  17P GAIN WILD-TYPE 407 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     38   16
  17P GAIN WILD-TYPE  407  103
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                38                407
  YES               16                103
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED      14                         3
  17P GAIN WILD-TYPE   120                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0    38
  17P GAIN WILD-TYPE                                         1   354
D30V11, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                                   14                120
  BLACK OR AFRICAN AMERICAN                                3                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   38                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  34
  17P GAIN WILD-TYPE  11 370
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   34
  17P GAIN WILD-TYPE   11  370
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               34                370
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    63  42
  17Q GAIN WILD-TYPE 291 203
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               105                494 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                42                203 
$`17Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4460 
       60.39        18.28        24.00        35.97        27.12        21.99 
TCGA-CG-4475 TCGA-EQ-A4SO TCGA-2H-A9GF TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D 
       22.98        16.24        25.78        35.21         0.53        17.03 
TCGA-IG-A625 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H 
       12.82        23.18        31.56        25.22        30.25         0.30 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A88Z TCGA-L5-A8NE 
       18.35         3.32         1.38         4.90         7.40        55.50 
TCGA-L5-A8NN TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 
        5.49        13.38        13.15        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-R6-A6DN 
       12.59        12.00        12.33        13.18        12.26         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
        7.59         5.06        38.40         3.42        15.35         9.27 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7I TCGA-Z6-A8JE 
        1.55        18.31        33.70        46.19        15.91         2.10 
TCGA-3M-AB46 TCGA-B7-5818 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 
       58.03        11.70        14.43        11.44        29.42         2.66 
TCGA-BR-8369 TCGA-BR-8686 TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4QI 
       14.04        20.88        12.89         0.53        20.42        21.44 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-5719 TCGA-CG-5722 
        6.31        12.43         7.99        12.03         1.02         0.99 
TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8573 TCGA-D7-A6EY 
       12.03        18.54        13.35        12.79        19.50        11.44 
TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-7916 TCGA-HJ-7597 
       22.29         0.62        72.23        19.53        14.07        26.47 
TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
       22.82        22.75        33.40        18.81        18.38        13.35 
TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-MX-A666 TCGA-R5-A7ZR 
        6.44        10.62        11.70        15.75        14.04         6.08 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91V 
       13.25        13.02        18.48        73.41        20.81        42.64 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.56         9.04         2.01         4.54        66.81        21.04 
TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6F 
       42.54        43.66        54.12 

$`17Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        34.85         4.31         8.94         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-5727 
       22.82         0.36         5.16        20.02        47.05        79.07 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH 
        0.23        20.15         9.86        27.35        26.93        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OF 
       47.38        21.70        24.03         6.28         3.16        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       32.61        21.01        47.93         7.17         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        12.33        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 
       13.25        12.62        12.46        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       25.25        10.52        12.23        12.03        13.18        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
        0.13        12.03        12.85        33.11         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW 
        8.98        25.81        27.09        22.82        12.43         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        18.18        52.27        18.05        11.24         9.17 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       18.21        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98         1.48        27.55        28.57         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65         1.15        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 
        6.97        36.00         0.99         6.02       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        17.19        10.26        15.22        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       12.36        11.31        12.33        24.72        16.80        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.31        20.32        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.13         7.99        14.47        21.27        11.38         3.48 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ 
       14.07        15.68        36.36         3.45         3.39        12.46 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1X TCGA-IP-7968 
       19.53         6.74        12.59         6.51        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 
        1.71        60.85         9.50         9.73        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        5.72         2.66        11.24        18.41        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        17.13        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               0.3                0.0 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             73.41             122.30 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             14.04              13.87 
[1] "0.3 - 73.4 (14.0)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         3        3        8        3        17        15
  17Q GAIN WILD-TYPE       7       18       39       30        70        72
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED          10         14          9          6       11
  17Q GAIN WILD-TYPE        18         81         63         40       38
                    vv
clus                 STAGE IVA
  17Q GAIN MUTATED           0
  17Q GAIN WILD-TYPE         4
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  3                 18
  STAGE IB                  8                 39
  STAGE II                  3                 30
  STAGE IIA                17                 70
  STAGE IIB                15                 72
  STAGE III                10                 18
  STAGE IIIA               14                 81
  STAGE IIIB                9                 63
  STAGE IIIC                6                 40
  STAGE IV                 11                 38
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17Q GAIN MUTATED      11  26  49  16
  17Q GAIN WILD-TYPE    44 110 234 108
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1               11                 44
  T2                  26                110
  T3                  49                234
  T4                  16                108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q GAIN MUTATED    36  34  14  15
  17Q GAIN WILD-TYPE 171 153  84  81
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               36                171
  N1               34                153
  N2               14                 84
  N3               15                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    82   9
  17Q GAIN WILD-TYPE 442  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     82    9
  17Q GAIN WILD-TYPE  442   30
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               82                442
  1                9                 30
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    21  87
  17Q GAIN WILD-TYPE 164 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     21   87
  17Q GAIN WILD-TYPE  164  353
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               21                164
  MALE                 87                353
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    66  31
  17Q GAIN WILD-TYPE 379  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     66   31
  17Q GAIN WILD-TYPE  379   88
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                66                379
  YES               31                 88
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED      23                         7
  17Q GAIN WILD-TYPE   111                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    67
  17Q GAIN WILD-TYPE                                         1   325
D31V11, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                                   23                111
  BLACK OR AFRICAN AMERICAN                                7                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   67                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  62
  17Q GAIN WILD-TYPE  10 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   62
  17Q GAIN WILD-TYPE   10  342
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               62                342
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    71  59
  18P GAIN WILD-TYPE 283 186
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               130                469 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                59                186 
$`18P GAIN MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A88Y TCGA-L5-A8NT 
       60.39        34.85         4.31         8.94         0.36        27.12 
TCGA-CG-4460 TCGA-CG-4475 TCGA-MX-A663 TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ 
       21.99        22.98         9.86         7.63        13.94         4.21 
TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A97I TCGA-JY-A6FE TCGA-L5-A4OM TCGA-L5-A4ON 
        0.53        12.82        12.16         3.68        47.93        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A8NN 
        1.38         3.16         4.90         7.13         2.60         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49S TCGA-LN-A49U 
       21.37        13.41        83.24        46.09        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4MQ 
       12.59        13.25        12.62        12.76        12.59        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A9FR TCGA-R6-A6KZ 
       13.22         4.47        12.33        25.25        12.26         5.06 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EQ TCGA-VR-A8EX 
       12.69        20.38         3.42        16.44        22.82        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-BR-4184 
       18.18        52.27        11.24        25.08         2.10         6.97 
TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6565 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-8060 
       18.35         9.67         9.17        15.32         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 
        0.69         9.60         8.05        29.42         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        7.40        13.08         3.32         9.21        20.22         1.12 
TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
        8.22        13.87         0.72        13.51        20.65         1.15 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-A486 TCGA-CD-A4MH 
       13.41        13.02        13.15        12.10         6.31        12.20 
TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       12.03        20.91        17.19        10.26        15.22        12.79 
TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       14.66        13.78        11.31        22.29        15.65        19.96 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 
        0.56         5.52         6.21        63.06        26.47         5.92 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI 
        0.76        22.75        25.81        23.80        33.40        18.38 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A666 
       19.53         6.44         6.74        10.62        63.62        14.04 
TCGA-R5-A7ZI TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
       74.53        35.61         0.92        21.73        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91U 
       17.85         1.87         9.27        21.83        18.74         1.71 
TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
        9.04        43.66        38.93         0.79 

$`18P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        18.28        24.00         4.70        19.99        22.82 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-5727 TCGA-EQ-A4SO 
       35.97         5.16        20.02        47.05        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
        0.23        20.15        27.35        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       14.30        58.55         5.92         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       23.41         9.96        14.86         4.67        14.50       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP 
        0.30        26.33        32.61        21.01         3.32         7.17 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
       58.59        29.00         7.43        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NV 
       16.47        13.55        13.22         7.76         8.71        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.41        12.33        13.38        12.46        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HW 
       22.39        12.85        15.52        11.54        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB 
        9.30        15.78         2.89         2.30         7.00         5.29 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G 
        1.55        18.31         8.12        33.70        46.19        18.05 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        18.21        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
        7.43        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 
       35.84        33.63        39.78        18.15        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 
       29.56        33.21        37.25        14.43        29.59        32.25 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        0.56         2.66        19.96         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        5.39        25.18        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
        9.86        20.88        10.68        34.13         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 
       20.42        21.44        16.14         5.13        13.18        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       11.21        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       18.61        17.85        13.35        15.98        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 
       14.76        26.43        11.24        11.44        20.32         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7134 
       17.06        59.54         5.03        13.58        77.29        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81         3.39        12.46        13.35 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
        5.56        37.64        36.95         3.72        19.73        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        43.36        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       73.41        39.45        11.70        61.22        20.81        32.88 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 
       42.64        60.85         9.50         9.73        55.56         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        42.54        11.24        18.41        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.36               0.00 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             83.24             122.30 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            12.775             14.790 
[1] "0.4 - 83.2 (12.8)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         2        4       10        6        18        20
  18P GAIN WILD-TYPE       8       17       37       27        69        67
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED          10         17         11         14       12
  18P GAIN WILD-TYPE        18         78         61         32       37
                    vv
clus                 STAGE IVA
  18P GAIN MUTATED           1
  18P GAIN WILD-TYPE         3
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  4                 17
  STAGE IB                 10                 37
  STAGE II                  6                 27
  STAGE IIA                18                 69
  STAGE IIB                20                 67
  STAGE III                10                 18
  STAGE IIIA               17                 78
  STAGE IIIB               11                 61
  STAGE IIIC               14                 32
  STAGE IV                 12                 37
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18P GAIN MUTATED      15  25  62  27
  18P GAIN WILD-TYPE    40 111 221  97
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1               15                 40
  T2                  25                111
  T3                  62                221
  T4                  27                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P GAIN MUTATED    43  44  17  25
  18P GAIN WILD-TYPE 164 143  81  71
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               43                164
  N1               44                143
  N2               17                 81
  N3               25                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   108   9
  18P GAIN WILD-TYPE 416  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    108    9
  18P GAIN WILD-TYPE  416   30
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0              108                416
  1                9                 30
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    40  95
  18P GAIN WILD-TYPE 145 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     40   95
  18P GAIN WILD-TYPE  145  345
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               40                145
  MALE                 95                345
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    94  29
  18P GAIN WILD-TYPE 351  90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     94   29
  18P GAIN WILD-TYPE  351   90
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                94                351
  YES               29                 90
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED      30                         2
  18P GAIN WILD-TYPE   104                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           0    85
  18P GAIN WILD-TYPE                                         1   307
D32V11, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                                   30                104
  BLACK OR AFRICAN AMERICAN                                2                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   85                307
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3  82
  18P GAIN WILD-TYPE   8 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3   82
  18P GAIN WILD-TYPE    8  322
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               82                322
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    43  32
  18Q GAIN WILD-TYPE 311 213
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                75                524 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                32                213 
$`18Q GAIN MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-CG-4460 TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       60.39         0.36        21.99         7.63         5.92        13.94 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A625 TCGA-JY-A6FE TCGA-L5-A43E TCGA-L5-A4OR 
        4.21        33.27        12.82         3.68        30.25         3.16 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HY TCGA-LN-A9FR 
        5.49        21.37        12.62        12.76        12.03        12.26 
TCGA-R6-A6KZ TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-VR-AA7B 
        5.06        20.38         3.42        22.82        52.27        11.24 
TCGA-Z6-A8JE TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6565 TCGA-BR-7901 TCGA-BR-8077 
        2.10         6.97         9.67         9.17         3.45         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        9.60         8.05        29.42         2.20        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 
       13.08        25.18         1.12         1.48         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 
       20.65         1.15        13.41        13.02        13.15        12.10 
TCGA-D7-5579 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-FP-8631 
       20.91        15.22        12.79        13.78        11.31         0.56 
TCGA-FP-A4BF TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GD 
        5.52        63.06        26.47         5.92         0.76        22.75 
TCGA-HU-A4GF TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-MX-A666 
       25.81        23.80        33.40        18.38        19.53        14.04 
TCGA-R5-A7ZI TCGA-RD-A8N9 TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A91E 
       74.53        35.61         2.70         1.87         9.27        21.83 
TCGA-VQ-A91N TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       18.74        43.66         0.79 

$`18Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       20.15         9.86        27.35        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
       14.30        58.55         8.94        16.24        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55        13.22         7.76         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.46        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
       15.78         2.89         2.30        12.69         7.00         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       18.18        46.19        18.05         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       19.73        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       33.63        39.78        18.15        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       29.56        33.21        37.25        14.43        11.44        29.59 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 
       32.25         0.56         2.66        19.96         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
       25.05         3.72         5.39         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
       28.34         0.66        32.52         0.46        20.42        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
       16.14         5.13        13.18        13.35        11.21        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM 
       22.29        17.06        59.54         5.03        13.58         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       77.29        52.21        30.51         1.51        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.32        22.82        21.07        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.26        22.68        24.20         3.25        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
       63.62        37.64        36.95         3.72        19.73        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       22.19         2.50        12.79        17.85        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        61.22        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        11.24        18.41        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.36               0.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             74.53             122.30 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             12.76              14.40 
[1] "0.4 - 74.5 (12.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         3        2        5        5         7         8
  18Q GAIN WILD-TYPE       7       19       42       28        80        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           8         11          6         10        8
  18Q GAIN WILD-TYPE        20         84         66         36       41
                    vv
clus                 STAGE IVA
  18Q GAIN MUTATED           0
  18Q GAIN WILD-TYPE         4
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  2                 19
  STAGE IB                  5                 42
  STAGE II                  5                 28
  STAGE IIA                 7                 80
  STAGE IIB                 8                 79
  STAGE III                 8                 20
  STAGE IIIA               11                 84
  STAGE IIIB                6                 66
  STAGE IIIC               10                 36
  STAGE IV                  8                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18Q GAIN MUTATED       8  12  30  25
  18Q GAIN WILD-TYPE    47 124 253  99
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                8                 47
  T2                  12                124
  T3                  30                253
  T4                  25                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q GAIN MUTATED    24  23  11  16
  18Q GAIN WILD-TYPE 183 164  87  80
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               24                183
  N1               23                164
  N2               11                 87
  N3               16                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    63   5
  18Q GAIN WILD-TYPE 461  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     63    5
  18Q GAIN WILD-TYPE  461   34
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               63                461
  1                5                 34
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    26  53
  18Q GAIN WILD-TYPE 159 387
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     26   53
  18Q GAIN WILD-TYPE  159  387
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               26                159
  MALE                 53                387
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    59  12
  18Q GAIN WILD-TYPE 386 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     59   12
  18Q GAIN WILD-TYPE  386  107
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                59                386
  YES               12                107
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED      17                         1
  18Q GAIN WILD-TYPE   117                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           0    50
  18Q GAIN WILD-TYPE                                         1   342
D33V11, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                                   17                117
  BLACK OR AFRICAN AMERICAN                                1                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   50                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1  53
  18Q GAIN WILD-TYPE  10 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   53
  18Q GAIN WILD-TYPE   10  351
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               53                351
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    52  25
  19P GAIN WILD-TYPE 302 220
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                77                522 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                25                220 
$`19P GAIN MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       24.00        35.97        27.12        47.05        21.99        22.98 
TCGA-EQ-A4SO TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-IG-A3QL TCGA-L5-A43C TCGA-L5-A4OO 
       16.24        58.55         8.94        35.21         3.16         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V 
        1.38         3.16        10.36         5.92        13.15        12.59 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       25.25        12.00        13.18         0.13        12.85        12.26 
TCGA-R6-A6XG TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EX 
       38.40        12.69        20.38        15.35        27.09        28.11 
TCGA-X8-AAAR TCGA-B7-A5TK TCGA-BR-4253 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7959 
       18.21         9.47         4.08        17.29        19.33        33.21 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8370 TCGA-BR-A453 TCGA-BR-A4J8 TCGA-BR-A4QI 
       29.42        19.96         3.32         6.08        13.51        21.44 
TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48C TCGA-CG-4449 
       13.18        12.53        12.39        12.82        11.61        19.07 
TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        0.99         4.01        25.71        19.13        20.55        18.54 
TCGA-D7-6528 TCGA-D7-8578 TCGA-D7-A4YU TCGA-FP-7916 TCGA-FP-A4BF TCGA-HF-7133 
       15.22        21.14        16.44        14.07         5.52        63.06 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4H2 TCGA-HU-A4H6 
       28.96        22.82        24.30        22.75        12.95        21.17 
TCGA-IN-7808 TCGA-IN-A6RP TCGA-MX-A666 TCGA-SW-A7EB TCGA-VQ-A8E3 TCGA-VQ-A8PE 
        3.45         6.44        14.04         5.79        21.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A91A TCGA-VQ-A91S TCGA-VQ-A925 TCGA-VQ-A92D 
       12.79        39.45        32.88         4.54        66.81 

$`19P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        19.99        22.82         0.36         5.16        20.02 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07         0.23        20.15         9.86        27.35        26.93 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       26.33        32.61        21.01        47.93        18.35         7.17 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.85        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       13.41        12.33        13.38        15.35        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        10.52        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.38        12.03        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89         2.30         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       16.44         9.27         8.98        25.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       46.19        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       19.73        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 
        9.60        32.25         8.05         0.56         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.30        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        29.98        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       28.96        65.10        69.04        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.91        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        0.56         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
        1.51         5.92        24.39        18.15        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        14.07        15.68        33.40        36.36 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       43.36        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.29        46.26        16.31         2.50         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        73.41        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        20.81         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.73        55.56         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.13               0.00 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             66.81             122.30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             16.24              13.63 
[1] "0.1 - 66.8 (16.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         1        1        5        3        13        10
  19P GAIN WILD-TYPE       9       20       42       30        74        77
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           2         15         11          5        6
  19P GAIN WILD-TYPE        26         80         61         41       43
                    vv
clus                 STAGE IVA
  19P GAIN MUTATED           1
  19P GAIN WILD-TYPE         3
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  1                 20
  STAGE IB                  5                 42
  STAGE II                  3                 30
  STAGE IIA                13                 74
  STAGE IIB                10                 77
  STAGE III                 2                 26
  STAGE IIIA               15                 80
  STAGE IIIB               11                 61
  STAGE IIIC                5                 41
  STAGE IV                  6                 43
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19P GAIN MUTATED       5  22  42   9
  19P GAIN WILD-TYPE    50 114 241 115
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                5                 50
  T2                  22                114
  T3                  42                241
  T4                   9                115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P GAIN MUTATED    23  24  12  17
  19P GAIN WILD-TYPE 184 163  86  79
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               23                184
  N1               24                163
  N2               12                 86
  N3               17                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    62   7
  19P GAIN WILD-TYPE 462  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     62    7
  19P GAIN WILD-TYPE  462   32
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               62                462
  1                7                 32
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    22  61
  19P GAIN WILD-TYPE 163 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     22   61
  19P GAIN WILD-TYPE  163  379
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               22                163
  MALE                 61                379
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    59  17
  19P GAIN WILD-TYPE 386 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     59   17
  19P GAIN WILD-TYPE  386  102
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                59                386
  YES               17                102
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED      22                         2
  19P GAIN WILD-TYPE   112                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           0    47
  19P GAIN WILD-TYPE                                         1   345
D34V11, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                                   22                112
  BLACK OR AFRICAN AMERICAN                                2                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   47                345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  55
  19P GAIN WILD-TYPE  10 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   55
  19P GAIN WILD-TYPE   10  349
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               55                349
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    66  46
  19Q GAIN WILD-TYPE 288 199
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               112                487 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                46                199 
$`19Q GAIN MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       24.00        35.97        27.12        47.05        21.99        22.98 
TCGA-EQ-A4SO TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3QL 
       16.24        58.55         7.63         8.94        16.24        35.21 
TCGA-IG-A4QS TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OQ 
        3.88         3.16        26.33        32.61         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        3.16        13.55         5.49        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49U TCGA-LN-A4A6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO 
        5.92        15.35        12.85        25.25        12.00         0.13 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A8WG 
       12.85        12.26         5.06        16.31        38.40        12.69 
TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-AA7I TCGA-X8-AAAR 
       20.38        15.35        27.09        28.11        15.91        18.21 
TCGA-Z6-A8JE TCGA-B7-A5TK TCGA-BR-4253 TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-7959 
        2.10         9.47         4.08        19.33        39.78        33.21 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8690 
       29.42        19.96         3.32         9.21         1.12        10.68 
TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 
        6.08         0.72        13.51        21.44        13.18        12.76 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48C TCGA-CG-4438 TCGA-CG-5722 
       12.53        12.39        12.82        11.61        54.08         0.99 
TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6818 TCGA-D7-6822 
        4.01        25.71        19.13        18.54        12.36        12.33 
TCGA-D7-8570 TCGA-D7-8578 TCGA-D7-A4YU TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7916 
       24.72        21.14        16.44         7.99        72.23        14.07 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
        5.52         6.21        63.06        24.39        28.96        22.82 
TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7808 
       24.30        22.75         2.10        12.95        21.17         3.45 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7ZR TCGA-RD-A7BT 
       13.35         6.44        63.62        14.04         6.08         8.61 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
       35.61         5.79        13.25        21.73         7.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A91A TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A923 TCGA-VQ-A925 
       12.79        39.45        32.88         1.71         2.01         4.54 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA6F TCGA-VQ-AA6K 
       66.81        11.24        54.12        12.43 

$`19Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        19.99        22.82         0.36         5.16        20.02 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07         0.23        20.15         9.86        27.35        26.93 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       25.78        31.27        14.30         5.92        13.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28        30.25         0.30        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G 
        7.76        21.37         8.71        13.41        83.24        10.85 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX 
       12.33        13.22         4.47        12.33        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38        13.18        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ 
       33.11         7.82         8.02         7.59         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         2.30         7.00 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44         9.27         8.98        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       19.73        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       33.63        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 
        9.60        32.25         8.05         0.56         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86        20.88         8.22        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.59         7.17        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         6.02       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        65.10        69.04        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       12.66        20.91        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       11.31        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       14.47        21.27        11.38         3.48        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 
       17.06        59.54         5.03        13.58         0.56        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 
       52.21        30.51        26.47         1.51         5.92        18.15 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.32        21.07         0.76         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       36.36        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       19.73        45.67        18.21         8.52        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       16.87        19.04         0.92        48.79         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       18.48        43.36        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.29        46.26        16.31         2.50         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        73.41        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        20.81        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
       55.56         9.04        55.43         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       32.94        17.13        26.04        16.14        27.55        17.26 
TCGA-ZQ-A9CR 
        0.79 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.13               0.00 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             72.23             122.30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             13.53              14.01 
[1] "0.1 - 72.2 (13.5)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1"  
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         2        3        8        5        15        13
  19Q GAIN WILD-TYPE       8       18       39       28        72        74
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           6         22         15          8        8
  19Q GAIN WILD-TYPE        22         73         57         38       41
                    vv
clus                 STAGE IVA
  19Q GAIN MUTATED           2
  19Q GAIN WILD-TYPE         2
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  3                 18
  STAGE IB                  8                 39
  STAGE II                  5                 28
  STAGE IIA                15                 72
  STAGE IIB                13                 74
  STAGE III                 6                 22
  STAGE IIIA               22                 73
  STAGE IIIB               15                 57
  STAGE IIIC                8                 38
  STAGE IV                  8                 41
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19Q GAIN MUTATED      10  26  61  15
  19Q GAIN WILD-TYPE    45 110 222 109
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1               10                 45
  T2                  26                110
  T3                  61                222
  T4                  15                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q GAIN MUTATED    32  38  15  24
  19Q GAIN WILD-TYPE 175 149  83  72
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               32                175
  N1               38                149
  N2               15                 83
  N3               24                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    93   8
  19Q GAIN WILD-TYPE 431  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     93    8
  19Q GAIN WILD-TYPE  431   31
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               93                431
  1                8                 31
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    29  90
  19Q GAIN WILD-TYPE 156 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     29   90
  19Q GAIN WILD-TYPE  156  350
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               29                156
  MALE                 90                350
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    86  23
  19Q GAIN WILD-TYPE 359  96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     86   23
  19Q GAIN WILD-TYPE  359   96
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                86                359
  YES               23                 96
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED      27                         4
  19Q GAIN WILD-TYPE   107                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           1    70
  19Q GAIN WILD-TYPE                                         0   322
D35V11, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                                   27                107
  BLACK OR AFRICAN AMERICAN                                4                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   70                322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  73
  19Q GAIN WILD-TYPE  10 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   73
  19Q GAIN WILD-TYPE   10  331
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               73                331
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   191 148
  20P GAIN WILD-TYPE 163  97
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               339                260 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               148                 97 
$`20P GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.31        24.00         4.70         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       20.02        47.05        79.07         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       27.35        25.78        31.27         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85         2.63        20.12         3.88         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE 
       23.41         4.67        14.50        12.16       122.10         3.68 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        31.56        25.22         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        0.30        47.93        18.35         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NN 
        7.40        55.50         2.66        12.92        16.47         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        13.41        52.57        46.09        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4A2 
       10.45        12.33        13.38        13.15        12.62        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX 
       12.76        12.85        11.54        12.33        25.25        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6DN 
       13.18        12.33        13.18         0.13        12.85         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06        16.31         7.04         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       15.78         2.89        12.69         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
        9.27         8.98        27.09         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       15.91        25.08         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.73        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4280 
        4.64        18.35        30.90         4.08         9.67         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 
       15.95        13.87        13.68        19.33        39.12         9.17 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       18.05        19.89        40.21        21.90         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 
       33.63        18.15        15.32        28.73         3.45        29.56 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8291 
       33.21        11.44         0.69         9.60         0.56        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 
        2.20        15.58         7.40        14.04        14.79         7.36 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        27.12         9.34 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        7.53        26.73        24.79         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       10.68        13.87         7.53        34.98         1.48         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.53        13.51         0.46        20.42         1.15        21.44 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.02        13.15        13.18        12.76        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
       12.33        12.30        12.39        11.64        15.39        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 
       11.77        20.02        27.02        15.95         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        4.01        14.01        12.03        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
       30.97        36.00         1.02         0.99        12.03        28.96 
TCGA-CG-5730 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
        4.01         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 
       18.54        13.35        17.19        10.26        15.22        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8579 TCGA-D7-A4YT 
       11.31        12.33        24.72        19.50        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       16.44         5.92        36.43        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-8122 
       20.32        22.29        15.65         8.38        19.96         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HJ-7597 TCGA-HU-8238 
       17.06         0.56         5.52         6.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        24.39        18.15        21.07         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.26         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI 
       23.84        21.17        33.40        36.36         3.45        18.38 
TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
       13.35         6.74        12.59        10.62        11.70        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        5.56        63.62        37.64        14.04        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 
       74.53         6.08         9.24         8.61        16.67       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       57.44         8.94        35.61         5.79        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       43.36        21.73        46.26        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
        2.70        17.85        15.65        64.57        73.41        39.45 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       21.83        18.74        32.88         1.71        60.85         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.56         9.04         2.01         5.72        66.81        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G 
       42.54        11.24        18.41        38.93        32.94        26.04 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

$`20P GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         8.94        19.99 
TCGA-L5-A88T TCGA-Q9-A6FU TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-VQ-A94U 
       22.82         5.16        21.99        22.98        16.24        26.93 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT 
       14.30        58.55         7.63        20.78        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD 
        0.79        12.82         9.96        14.86        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OH 
       41.52        47.38        24.03         6.28        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 
       21.01         3.32         3.16        25.12         3.75         3.02 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.48        13.55        13.22         7.76        21.37        83.24 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V 
        5.92        12.66        12.43        13.41        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       13.25        12.46        12.59        12.59        22.39        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
       12.33        13.22         4.47        10.52        12.00        12.03 
TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6XG 
       13.38        12.03        12.26        33.11         7.82        38.40 
TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO 
       53.95         2.30         7.00        20.38        15.35        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-AA4G TCGA-X8-AAAR TCGA-XP-A8T7 
       22.82        12.43        18.31        18.05        18.21        41.23 
TCGA-XP-A8T8 TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 
       14.37        58.03        26.70        11.70        19.56         7.43 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6456 
        4.08         9.34         6.18         9.57        34.68        17.29 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       26.10        32.78        25.61        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7957 
       31.20        44.94        36.16        35.84        39.78         9.07 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       37.25        14.43        29.59        32.25         8.05        29.42 
TCGA-BR-8289 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.66         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 
       31.27        25.05         3.72         1.12        12.79        28.14 
TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
        6.28        31.96        32.58        34.13         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       28.57        12.89         8.98        14.17        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5802 
       32.52        20.65        16.14         5.13        13.41        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-8536 
       11.21        12.10        12.59        12.59        12.07        12.43 
TCGA-CD-A489 TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 
       11.31        12.62         3.02         1.02         8.05        29.98 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
       19.07         0.00         9.01         6.97         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-6519 
      105.07        15.02        65.10        69.04        21.07        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8572 
       18.84        18.61        17.85        15.98        12.79        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YY TCGA-D7-A4Z0 
       17.19        18.21        14.66        21.14        13.78        14.76 
TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7735 
       11.44         4.34         7.13         0.62        21.27         3.48 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       59.54         5.03        13.58        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G3 TCGA-HU-A4G8 
       30.51        28.96        22.32        22.82         5.59        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H5 
       24.20        21.37        29.98         6.51        29.00        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
       14.07        15.68        18.81         3.39        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG 
        6.44         6.51        15.75         2.53        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
       19.73        45.67         4.60        11.05         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA 
       37.91        40.64       116.38        71.38        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        48.79         5.46        18.48        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM 
       37.22         7.73        30.97        34.29        16.31         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91D 
        9.27        23.41        13.35        29.59        14.33        11.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A925 
       61.22        20.81        42.64         9.50        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F 
        6.58         2.66        43.66        28.41        17.13        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J 
       16.14        27.55 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               0.1                0.0 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             122.1              122.3 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            13.020             15.865 
[1] "0.1 - 122.1 (13.0)" "0.0 - 122.3 (15.9)"
[1] "hr=" "1.4"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         4       11       22       17        46        47
  20P GAIN WILD-TYPE       6       10       25       16        41        40
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED          16         60         41         27       23
  20P GAIN WILD-TYPE        12         35         31         19       26
                    vv
clus                 STAGE IVA
  20P GAIN MUTATED           4
  20P GAIN WILD-TYPE         0
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   4                  6
  STAGE IA                 11                 10
  STAGE IB                 22                 25
  STAGE II                 17                 16
  STAGE IIA                46                 41
  STAGE IIB                47                 40
  STAGE III                16                 12
  STAGE IIIA               60                 35
  STAGE IIIB               41                 31
  STAGE IIIC               27                 19
  STAGE IV                 23                 26
  STAGE IVA                 4                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20P GAIN MUTATED      30  70 167  62
  20P GAIN WILD-TYPE    25  66 116  62
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               30                 25
  T2                  70                 66
  T3                 167                116
  T4                  62                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P GAIN MUTATED   103 113  52  53
  20P GAIN WILD-TYPE 104  74  46  43
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              103                104
  N1              113                 74
  N2               52                 46
  N3               53                 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"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   290  20
  20P GAIN WILD-TYPE 234  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    290   20
  20P GAIN WILD-TYPE  234   19
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              290                234
  1               20                 19
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    88 261
  20P GAIN WILD-TYPE  97 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     88  261
  20P GAIN WILD-TYPE   97  179
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               88                 97
  MALE                261                179
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   259  55
  20P GAIN WILD-TYPE 186  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    259   55
  20P GAIN WILD-TYPE  186   64
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               259                186
  YES               55                 64
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED      74                         9
  20P GAIN WILD-TYPE    60                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           1   221
  20P GAIN WILD-TYPE                                         0   171
D36V11, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                                   74                 60
  BLACK OR AFRICAN AMERICAN                                9                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  221                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"
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     6 227
  20P GAIN WILD-TYPE   5 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      6  227
  20P GAIN WILD-TYPE    5  177
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  5
  NOT HISPANIC OR LATINO              227                177
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   219 164
  20Q GAIN WILD-TYPE 135  81
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               383                216 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               164                 81 
$`20Q GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.31        24.00         4.70         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        27.35        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45         7.69        33.27         0.85         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H 
        3.88         0.53        17.03        23.41         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       12.16       122.10         3.68        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       25.22         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ 
        2.60         7.40        55.50         2.66        12.92        16.47 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
       13.22         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49P TCGA-LN-A49R 
       46.09        10.85        10.36        10.45        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.15        12.59        12.62        12.49        12.76        12.85 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        25.25        12.23        12.03        13.18        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       13.18         0.13        12.85         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW 
       16.44         9.27         8.98        27.09         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 
       28.11        52.27        46.19        11.24         9.17        25.08 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-A5TJ 
        3.42         2.10         2.66        19.73        58.03        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
        9.47         9.44         6.61         6.97         4.64        18.35 
TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       30.90         4.08         9.67         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       18.05        19.89        40.21        21.90         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 
       33.63        18.15        15.32        28.73         3.45        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 
       33.21        14.43        11.44         0.69         9.60         0.56 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 
        2.66        19.96         2.20        15.58         7.40        14.04 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       14.79         7.36         5.39        25.18         9.21        20.22 
TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        9.34         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       20.88         8.22        10.68        13.87         7.53        34.98 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 
        1.48        12.89         0.72         0.53        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 
       20.65        20.42         1.15        21.44        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
       12.33        12.30        12.39        11.64        15.39        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       11.77        20.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 
       54.08         4.01        14.01        12.03        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 
       12.00        30.97        36.00         1.02         0.99        12.03 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 
       20.91        19.13        20.55        18.84        18.54        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        19.50        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET 
       20.91        14.27        16.44         5.92        36.43        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
       19.96         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF 
       19.53        14.07        22.29        17.06         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        6.21        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.30        24.26         3.25        22.75        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
       12.95        23.84        23.80        21.17        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS 
        3.45         3.39        18.38        13.35         6.74        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        11.70        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        6.08         8.61        16.67        37.91       115.69        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        35.61         5.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF 
       18.48        43.36        21.73        46.26        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A8PX TCGA-VQ-A8PY 
       12.79         2.70        17.85        15.65        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       73.41        39.45        21.83        18.74        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        2.01         4.54         5.72        66.81        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       11.24        18.41        43.66        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        27.55        12.43        17.26         0.79 

$`20Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         8.94        19.99 
TCGA-L5-A88T TCGA-Q9-A6FU TCGA-CG-4460 TCGA-VQ-A94U TCGA-2H-A9GL TCGA-IG-A3QL 
       22.82         5.16        21.99        26.93         5.92        35.21 
TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
       20.78        18.64         9.30         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93F 
       14.86        44.75        68.02        41.52        47.38        24.03 
TCGA-KH-A6WC TCGA-L5-A4OJ TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI 
        6.28        21.01        25.12         3.75         3.02        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       13.55         7.76        83.24         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 
       13.41        15.35        13.25        12.46        12.59        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       10.52        12.00        13.38        12.03        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EQ 
        7.82         2.30        20.38        15.35        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7I 
       12.43        18.31        33.70        18.18        18.05        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-B7-5816 TCGA-B7-5818 
       18.21        41.23        14.37         1.32        26.70        11.70 
TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       19.56         7.43         4.08         9.34         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       34.68        32.78        25.61        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7957 
       31.20        44.94        36.16        35.84        39.78         9.07 
TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8360 
       37.25        29.59        32.25         8.05        29.42         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 
       26.33         4.31         3.32        11.80        31.27        25.05 
TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 
        3.72         1.12        12.79        27.12        28.14         6.28 
TCGA-BR-8680 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       31.96        34.13         6.08        27.55        28.57         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM 
       14.17        28.34         0.66        32.52        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-8536 
       13.41        13.35        11.21        12.59        12.07        12.43 
TCGA-CD-A489 TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 
       11.31        12.62         3.02         1.02        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        0.00         9.01         6.97         0.99         6.02       105.07 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 
       15.02        65.10        21.07        18.61        17.85        12.79 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A748 
       17.19        18.21        13.78        14.76        11.44         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        7.13         0.62        21.27        59.54         5.03        13.58 
TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       77.29        30.51        22.32         5.59        22.68        24.20 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
       21.37        29.98         6.51        29.00        14.07        15.68 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-AB1V 
       18.81        12.46        19.53         6.44         6.51        15.75 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       36.95         3.72        19.73         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB 
        5.13       122.30        40.64       116.38        71.38        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       19.04         0.92        48.79        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO 
        7.73        30.97        34.29        16.31         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q 
       23.41        13.35        29.59        11.70        61.22        20.81 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6I 
       55.43         6.58         2.66        28.41        17.13        16.14 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               0.1                0.0 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             122.1              122.3 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            13.350             15.435 
[1] "0.1 - 122.1 (13.3)" "0.0 - 122.3 (15.4)"
[1] "hr=" "1.3"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         6       13       27       18        47        58
  20Q GAIN WILD-TYPE       4        8       20       15        40        29
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED          19         67         46         28       27
  20Q GAIN WILD-TYPE         9         28         26         18       22
                    vv
clus                 STAGE IVA
  20Q GAIN MUTATED           4
  20Q GAIN WILD-TYPE         0
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   6                  4
  STAGE IA                 13                  8
  STAGE IB                 27                 20
  STAGE II                 18                 15
  STAGE IIA                47                 40
  STAGE IIB                58                 29
  STAGE III                19                  9
  STAGE IIIA               67                 28
  STAGE IIIB               46                 26
  STAGE IIIC               28                 18
  STAGE IV                 27                 22
  STAGE IVA                 4                  0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20Q GAIN MUTATED      36  82 187  68
  20Q GAIN WILD-TYPE    19  54  96  56
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               36                 19
  T2                  82                 54
  T3                 187                 96
  T4                  68                 56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q GAIN MUTATED   115 126  66  58
  20Q GAIN WILD-TYPE  92  61  32  38
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              115                 92
  N1              126                 61
  N2               66                 32
  N3               58                 38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   325  22
  20Q GAIN WILD-TYPE 199  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    325   22
  20Q GAIN WILD-TYPE  199   17
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              325                199
  1               22                 17
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   100 295
  20Q GAIN WILD-TYPE  85 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    100  295
  20Q GAIN WILD-TYPE   85  145
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              100                 85
  MALE                295                145
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   289  68
  20Q GAIN WILD-TYPE 156  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    289   68
  20Q GAIN WILD-TYPE  156   51
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               289                156
  YES               68                 51
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED      82                        12
  20Q GAIN WILD-TYPE    52                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           1   247
  20Q GAIN WILD-TYPE                                         0   145
D37V11, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                                   82                 52
  BLACK OR AFRICAN AMERICAN                               12                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  247                145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     8 251
  20Q GAIN WILD-TYPE   3 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8  251
  20Q GAIN WILD-TYPE    3  153
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                  3
  NOT HISPANIC OR LATINO              251                153
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    24  13
  21Q GAIN WILD-TYPE 330 232
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                37                562 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                232 
$`21Q GAIN MUTATED`
TCGA-S8-A6BV TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A93E 
       20.02         2.63        23.41         4.67        14.50        25.22 
TCGA-L5-A8NE TCGA-L5-A8NN TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 
       55.50         5.49        10.45        15.35        12.59        12.59 
TCGA-LN-A8I1 TCGA-V5-A7RC TCGA-VR-A8EP TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-BR-6456 
       13.18         3.42        27.09        18.21        25.08        17.29 
TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8486 TCGA-BR-8687 
        3.45         0.69        29.42         2.20        20.22         8.22 
TCGA-BR-A44U TCGA-CD-5799 TCGA-CD-A486 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6822 
       13.87        13.02         6.31        10.26        15.22        12.33 
TCGA-D7-A6F0 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4HD TCGA-IN-A6RP 
       22.29         5.92        22.75        11.77        33.40         6.44 
TCGA-VQ-A8PC 
       46.26 

$`21Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       16.24         0.23        20.15         9.86        27.35        26.93 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21         0.85        20.78        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        3.88         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       52.57        46.09        10.85        10.36         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W 
       12.43        13.41        12.33        13.38        13.15        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.38         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        15.91        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56         2.66        19.96        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 
       32.58         9.86        20.88        10.68        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       21.44        16.14         5.13        13.41        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82        12.43        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85        13.35        17.19        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       38.93        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.69               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              55.5              122.3 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            13.180             14.025 
[1] "0.7 - 55.5 (13.2)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1"  
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         0        2        3        3         8         7
  21Q GAIN WILD-TYPE      10       19       44       30        79        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           1          5          4          3        1
  21Q GAIN WILD-TYPE        27         90         68         43       48
                    vv
clus                 STAGE IVA
  21Q GAIN MUTATED           0
  21Q GAIN WILD-TYPE         4
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  2                 19
  STAGE IB                  3                 44
  STAGE II                  3                 30
  STAGE IIA                 8                 79
  STAGE IIB                 7                 80
  STAGE III                 1                 27
  STAGE IIIA                5                 90
  STAGE IIIB                4                 68
  STAGE IIIC                3                 43
  STAGE IV                  1                 48
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  21Q GAIN MUTATED       4   9  20   5
  21Q GAIN WILD-TYPE    51 127 263 119
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                4                 51
  T2                   9                127
  T3                  20                263
  T4                   5                119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q GAIN MUTATED    15  14   5   3
  21Q GAIN WILD-TYPE 192 173  93  93
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               15                192
  N1               14                173
  N2                5                 93
  N3                3                 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"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    35   1
  21Q GAIN WILD-TYPE 489  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     35    1
  21Q GAIN WILD-TYPE  489   38
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               35                489
  1                1                 38
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    10  29
  21Q GAIN WILD-TYPE 175 411
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10   29
  21Q GAIN WILD-TYPE  175  411
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               10                175
  MALE                 29                411
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    26   8
  21Q GAIN WILD-TYPE 419 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     26    8
  21Q GAIN WILD-TYPE  419  111
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                26                419
  YES                8                111
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED      13                         2
  21Q GAIN WILD-TYPE   121                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           0    23
  21Q GAIN WILD-TYPE                                         1   369
D38V11, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                                   13                121
  BLACK OR AFRICAN AMERICAN                                2                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   23                369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  32
  21Q GAIN WILD-TYPE  10 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   32
  21Q GAIN WILD-TYPE   10  372
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               32                372
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    41  20
  22Q GAIN WILD-TYPE 313 225
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                61                538 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                20                225 
$`22Q GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.31        27.12         5.16        35.21         0.85        20.78 
TCGA-IG-A97H TCGA-L5-A43E TCGA-L5-A4OM TCGA-LN-A49P TCGA-LN-A4A1 TCGA-LN-A4A2 
       14.50        30.25        47.93        12.33        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       12.59        12.85        11.54        12.33        13.22        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A8WG 
       12.00        12.23        12.33         0.13        12.85        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
       20.38         3.42        27.09         8.12        28.11        18.18 
TCGA-VR-AA7B TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7959 
       11.24        11.70         4.64        35.24        28.73        33.21 
TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4J8 TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 
       20.22         7.53        13.51        13.02        12.59        12.33 
TCGA-CG-4436 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4Z0 TCGA-D7-A6F0 
        7.99        18.54        15.98        14.66        14.76        22.29 
TCGA-F1-6875 TCGA-FP-7998 TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H5 
       72.23        22.29        22.82        11.77         6.58        23.80 
TCGA-IN-7808 TCGA-KB-A6F7 TCGA-RD-A8N6 TCGA-VQ-A8PJ TCGA-VQ-A91D TCGA-VQ-AA68 
        3.45        63.62         8.94         2.70        11.70        43.66 
TCGA-VQ-AA6K 
       12.43 

$`22Q GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV 
        4.70        19.99        22.82         0.36        35.97        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       20.15         9.86        27.35        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YB 
       16.24         4.21        32.45         7.69        33.27         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16         0.30        26.33        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 
       13.25        12.62        12.46        12.76        22.39        15.52 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
        4.47        25.25        10.52        12.03        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18        12.03        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         2.30         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 
       22.82        12.43         1.55        18.31        33.70        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        18.05         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        58.03        26.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         6.97         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       33.63        39.78        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       20.88         8.22        10.68        34.13        13.87         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       12.10        12.76        12.53         7.17        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        13.78        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        19.53        14.07        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        28.96        22.32        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       39.45        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.13               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             72.23             122.30 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             12.69              14.12 
[1] "0.1 - 72.2 (12.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         1        5        6        3        14         6
  22Q GAIN WILD-TYPE       9       16       41       30        73        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           2          7          6          5        2
  22Q GAIN WILD-TYPE        26         88         66         41       47
                    vv
clus                 STAGE IVA
  22Q GAIN MUTATED           1
  22Q GAIN WILD-TYPE         3
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  5                 16
  STAGE IB                  6                 41
  STAGE II                  3                 30
  STAGE IIA                14                 73
  STAGE IIB                 6                 81
  STAGE III                 2                 26
  STAGE IIIA                7                 88
  STAGE IIIB                6                 66
  STAGE IIIC                5                 41
  STAGE IV                  2                 47
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  22Q GAIN MUTATED       7  20  23  10
  22Q GAIN WILD-TYPE    48 116 260 114
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1                7                 48
  T2                  20                116
  T3                  23                260
  T4                  10                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q GAIN MUTATED    31  10   9   9
  22Q GAIN WILD-TYPE 176 177  89  87
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               31                176
  N1               10                177
  N2                9                 89
  N3                9                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    53   4
  22Q GAIN WILD-TYPE 471  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     53    4
  22Q GAIN WILD-TYPE  471   35
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               53                471
  1                4                 35
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    16  47
  22Q GAIN WILD-TYPE 169 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     16   47
  22Q GAIN WILD-TYPE  169  393
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               16                169
  MALE                 47                393
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    45  15
  22Q GAIN WILD-TYPE 400 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     45   15
  22Q GAIN WILD-TYPE  400  104
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                45                400
  YES               15                104
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED      25                         2
  22Q GAIN WILD-TYPE   109                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    32
  22Q GAIN WILD-TYPE                                         1   360
D39V11, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                                   25                109
  BLACK OR AFRICAN AMERICAN                                2                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   32                360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     2  46
  22Q GAIN WILD-TYPE   9 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   46
  22Q GAIN WILD-TYPE    9  358
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               46                358
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    38  34
  XP GAIN WILD-TYPE 316 211
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               72               527 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               34               211 
$`XP GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88Y TCGA-CG-4460 TCGA-CG-5727 TCGA-IG-A51D 
        4.31        19.99         0.36        21.99        79.07        17.03 
TCGA-JY-A6F8 TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49S 
      122.10         1.38         3.16         5.49        21.37        13.15 
TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A7HZ TCGA-LN-A8I1 
       12.59        12.49        12.59        11.54        13.18        13.18 
TCGA-LN-A9FQ TCGA-R6-A6L4 TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EY 
       12.85        16.31         2.89         3.42        15.35        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-XP-A8T6 TCGA-ZR-A9CJ TCGA-BR-4187 TCGA-BR-6801 
       18.18        46.19        25.08        19.73         4.64        40.21 
TCGA-BR-7197 TCGA-BR-7717 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8365 
        9.21        18.15        37.25        14.43         0.69        17.52 
TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CS TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MG 
       24.79         7.53         1.48        12.33        12.30         6.58 
TCGA-CG-4436 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5726 TCGA-D7-6519 TCGA-D7-8576 
        7.99        12.00        36.00        28.96        20.55        14.66 
TCGA-D7-A6EV TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-HF-7133 
       11.24         0.62         7.99        72.23         3.48        63.06 
TCGA-HF-7134 TCGA-HU-8244 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GF 
       52.21        24.39        24.30        24.26        24.20        25.81 
TCGA-HU-A4GT TCGA-HU-A4HD TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A8N6 TCGA-VQ-A8DT 
        6.51        33.40        18.21         8.61         8.94        48.79 
TCGA-VQ-A8E0 TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       18.48        14.33        21.83        20.81        32.88         1.71 

$`XP GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        22.82        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       27.35        26.93        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS 
       21.01        47.93        18.35         3.32         7.17        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.33        13.38        15.35        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.59        12.76        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        12.03        12.33        13.38         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G 
        1.55        18.31         8.12        28.11        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 
        3.42         2.10         1.32         2.66        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       36.16        35.24        35.84        33.63        39.78        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 
       28.73         3.45         9.07        29.56        33.21        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       31.10        13.08         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       20.88         8.22        10.68        34.13        13.87         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43         6.31        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 
        7.13        14.47        21.27        11.38        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.52         6.21        77.29        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        0.76         5.59        22.68         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.25        13.02        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N 
       64.57        73.41        39.45        11.70        61.22        18.74 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.36              0.00 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            122.1             122.3 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           15.005            13.780 
[1] "0.4 - 122.1 (15.0)" "0.0 - 122.3 (13.8)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         1        7        4        3        14         9
  XP GAIN WILD-TYPE       9       14       43       30        73        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           3          8          7          4        8
  XP GAIN WILD-TYPE        25         87         65         42       41
                   vv
clus                STAGE IVA
  XP GAIN MUTATED           0
  XP GAIN WILD-TYPE         4
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 7                14
  STAGE IB                 4                43
  STAGE II                 3                30
  STAGE IIA               14                73
  STAGE IIB                9                78
  STAGE III                3                25
  STAGE IIIA               8                87
  STAGE IIIB               7                65
  STAGE IIIC               4                42
  STAGE IV                 8                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XP GAIN MUTATED      10  17  31  13
  XP GAIN WILD-TYPE    45 119 252 111
D40V4, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  T0+T1              10                45
  T2                 17               119
  T3                 31               252
  T4                 13               111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XP GAIN MUTATED    33  18   9  10
  XP GAIN WILD-TYPE 174 169  89  86
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              33               174
  N1              18               169
  N2               9                89
  N3              10                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    61   2
  XP GAIN WILD-TYPE 463  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     61    2
  XP GAIN WILD-TYPE  463   37
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              61               463
  1               2                37
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    24  51
  XP GAIN WILD-TYPE 161 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     24   51
  XP GAIN WILD-TYPE  161  389
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              24               161
  MALE                51               389
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    51  18
  XP GAIN WILD-TYPE 394 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     51   18
  XP GAIN WILD-TYPE  394  101
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               51               394
  YES              18               101
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XP GAIN MUTATED      20                         7
  XP GAIN WILD-TYPE   114                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP GAIN MUTATED                                           1    37
  XP GAIN WILD-TYPE                                         0   355
D40V11, multiclass
                                           clus
vv                                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                                  20               114
  BLACK OR AFRICAN AMERICAN                               7                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  37               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     1  48
  XP GAIN WILD-TYPE  10 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1   48
  XP GAIN WILD-TYPE   10  356
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              48               356
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    50  39
  XQ GAIN WILD-TYPE 304 206
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               89               510 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               39               206 
$`XQ GAIN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88Y TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 
        4.31        19.99         0.36        20.02        21.99        79.07 
TCGA-2H-A9GI TCGA-IG-A3QL TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       14.30        35.21         3.88         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A4OQ 
        9.96         4.67       122.10        44.75        23.18         1.38 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49X 
        5.49        21.37         5.92        12.66        12.59        12.62 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FQ 
       12.49        12.59        11.54        13.18        13.18        12.85 
TCGA-LN-A9FR TCGA-R6-A6L4 TCGA-R6-A8W8 TCGA-V5-AASV TCGA-VR-A8EU TCGA-VR-A8EY 
       12.26        16.31         2.89        15.35        18.31        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-ZR-A9CJ TCGA-BR-4187 
       18.18        46.19        25.08        14.37        19.73         4.64 
TCGA-BR-6801 TCGA-BR-7717 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8362 
       40.21        18.15        37.25        14.43         0.69        13.08 
TCGA-BR-8365 TCGA-BR-8683 TCGA-BR-A452 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MG 
       17.52         9.86         7.53        12.33        12.30         6.58 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5726 TCGA-CG-5734 TCGA-D7-6526 TCGA-D7-6528 
       12.00        36.00        28.96         7.99        17.19        15.22 
TCGA-D7-6815 TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       15.98        11.24        15.65         0.62         7.99        72.23 
TCGA-FP-7735 TCGA-HF-7134 TCGA-HU-8244 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G9 
        3.48        52.21        24.39        24.30        24.26        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4HD TCGA-IN-7808 TCGA-R5-A7O7 
       22.75        25.81         6.51        33.40         3.45        45.67 
TCGA-RD-A7BT TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8PC TCGA-VQ-A8PY TCGA-VQ-A91E 
        8.61         8.94        48.79        46.26        14.33        21.83 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 
       32.88         1.71        55.56        66.81        43.66 

$`XQ GAIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 
        4.70        22.82        35.97        27.12         5.16        47.05 
TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       22.98        16.24         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       26.93        25.78        31.27        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        9.30         0.79        12.82        14.86        14.50        12.16 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D 
       68.02         3.68        41.52        47.38        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55        13.22         7.76         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N 
       52.57        46.09        10.85        10.36        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       13.41        12.33        13.38        13.15        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.59        12.76        22.39        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       12.00        12.23        12.03        12.33        13.38         0.13 
TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G 
       12.43         1.55         8.12        28.11        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD 
       11.24         9.17        15.91        18.21        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       36.16        35.24        35.84        33.63        39.78        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 
       28.73         3.45         9.07        29.56        33.21        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10         0.26        22.19         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53        26.73        24.79        31.96        32.58        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        10.68        34.13        13.87         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43         6.31        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       18.97         7.07        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04        21.07        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        10.26        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 
       22.29         8.38         4.34        19.96         7.13        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        30.51        26.47         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        5.59        22.68         3.25        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       15.68        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       63.62        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        30.97        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W 
       11.70        61.22        18.74        20.81        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.36              0.00 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            122.1             122.3 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           15.350            13.565 
[1] "0.4 - 122.1 (15.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         1        6        5        2        17        16
  XQ GAIN WILD-TYPE       9       15       42       31        70        71
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           4         12         11          5        8
  XQ GAIN WILD-TYPE        24         83         61         41       41
                   vv
clus                STAGE IVA
  XQ GAIN MUTATED           0
  XQ GAIN WILD-TYPE         4
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 6                15
  STAGE IB                 5                42
  STAGE II                 2                31
  STAGE IIA               17                70
  STAGE IIB               16                71
  STAGE III                4                24
  STAGE IIIA              12                83
  STAGE IIIB              11                61
  STAGE IIIC               5                41
  STAGE IV                 8                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XQ GAIN MUTATED      11  22  42  15
  XQ GAIN WILD-TYPE    44 114 241 109
D41V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1              11                44
  T2                 22               114
  T3                 42               241
  T4                 15               109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ GAIN MUTATED    36  30  14   9
  XQ GAIN WILD-TYPE 171 157  84  87
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              36               171
  N1              30               157
  N2              14                84
  N3               9                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    76   5
  XQ GAIN WILD-TYPE 448  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     76    5
  XQ GAIN WILD-TYPE  448   34
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              76               448
  1               5                34
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    26  67
  XQ GAIN WILD-TYPE 159 373
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     26   67
  XQ GAIN WILD-TYPE  159  373
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              26               159
  MALE                67               373
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    65  19
  XQ GAIN WILD-TYPE 380 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     65   19
  XQ GAIN WILD-TYPE  380  100
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               65               380
  YES              19               100
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED      29                         6
  XQ GAIN WILD-TYPE   105                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           1    48
  XQ GAIN WILD-TYPE                                         0   344
D41V11, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                                  29               105
  BLACK OR AFRICAN AMERICAN                               6                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  48               344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3  60
  XQ GAIN WILD-TYPE   8 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   60
  XQ GAIN WILD-TYPE    8  344
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              60               344
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    55  42
  1P LOSS WILD-TYPE 299 203
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               97               502 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               42               203 
$`1P LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG TCGA-EQ-A4SO 
       60.39         8.94        24.00         4.70        35.97        16.24 
TCGA-MX-A663 TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 
        9.86        14.30         7.63        16.24        32.45        33.27 
TCGA-IG-A4P3 TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88V 
       18.64        23.18         0.30         4.90        29.00         2.60 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-LN-A5U6 TCGA-LN-A5U7 
        7.40        55.50        12.92        16.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.00        13.18        12.33         8.02         7.59         5.06 
TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW 
        6.35         2.89         2.30        20.38        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8ER TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-B7-A5TJ TCGA-B7-A5TN 
        8.98        12.43        14.37         1.32        11.01         9.44 
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-7959 TCGA-BR-8289 
        6.61        17.29        19.33        35.24        33.21         2.66 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-A452 TCGA-BR-A4PE TCGA-BR-A4PF 
        9.21        24.79         9.86         7.53        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 
       21.44        13.02        13.35         7.17        15.39        12.82 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-5719 
        6.31        11.31        20.02         3.02        54.08         1.02 
TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 
       12.03         4.01        20.91        20.55        17.19        10.26 
TCGA-D7-6528 TCGA-D7-8573 TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-A4BF TCGA-HU-8249 
       15.22        19.50        19.96         0.62         5.52        28.96 
TCGA-HU-8604 TCGA-HU-A4HD TCGA-IN-AB1V TCGA-KB-A93H TCGA-R5-A7ZE TCGA-RD-A7BT 
       22.82        33.40        15.75        37.64        18.21         8.61 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A91A 
       13.25        13.02         7.73        22.19         2.70        39.45 
TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-AA6B TCGA-VQ-AA6K 
       55.56         4.54        66.81        21.04        32.94        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`1P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         4.31        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 
        0.36        27.12         5.16        20.02        47.05        21.99 
TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U 
       22.98        79.07         0.23        20.15        27.35        26.93 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         5.92        13.94         8.94 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21         7.69        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 
        7.13         7.43        15.48        25.12         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        2.66        13.48        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 
       13.22         4.47        10.52        12.23        12.03        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.82        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       15.78        12.69         7.00         5.29         3.42        15.35 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        22.82         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 
        3.42         2.10         2.66        19.73        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.70        19.56         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        7.36        25.05         3.72         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        7.53        26.73        31.96        32.58        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       20.65        16.14         5.13        13.41        13.15        13.18 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       11.21        12.10        12.76        12.59        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 
       12.30        12.39        12.59        11.64        12.07        12.43 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       12.62        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
       36.00         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
       22.29        15.65         8.38         4.34         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        18.15        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       37.22        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       13.35        29.59        64.57        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 
       42.64        60.85         9.50         9.73         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
       55.43         6.58         5.72         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        16.14        27.55        17.26 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              0.3               0.0 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            66.81            122.30 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           13.020            14.055 
[1] "0.3 - 66.8 (13.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         2        1        7        6        15         9
  1P LOSS WILD-TYPE       8       20       40       27        72        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           7         14          9          4       12
  1P LOSS WILD-TYPE        21         81         63         42       37
                   vv
clus                STAGE IVA
  1P LOSS MUTATED           1
  1P LOSS WILD-TYPE         3
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 1                20
  STAGE IB                 7                40
  STAGE II                 6                27
  STAGE IIA               15                72
  STAGE IIB                9                78
  STAGE III                7                21
  STAGE IIIA              14                81
  STAGE IIIB               9                63
  STAGE IIIC               4                42
  STAGE IV                12                37
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1P LOSS MUTATED       7  18  45  19
  1P LOSS WILD-TYPE    48 118 238 105
D42V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               7                48
  T2                 18               118
  T3                 45               238
  T4                 19               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P LOSS MUTATED    29  30  17  11
  1P LOSS WILD-TYPE 178 157  81  85
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              29               178
  N1              30               157
  N2              17                81
  N3              11                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"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    72  11
  1P LOSS WILD-TYPE 452  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     72   11
  1P LOSS WILD-TYPE  452   28
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              72               452
  1              11                28
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    26  71
  1P LOSS WILD-TYPE 159 369
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     26   71
  1P LOSS WILD-TYPE  159  369
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              26               159
  MALE                71               369
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    72  15
  1P LOSS WILD-TYPE 373 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     72   15
  1P LOSS WILD-TYPE  373  104
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               72               373
  YES              15               104
[1] 2 2
[1] FALSE
D42V9, continuous
D42V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED      19                         3
  1P LOSS WILD-TYPE   115                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           1    61
  1P LOSS WILD-TYPE                                         0   331
D42V11, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                                  19               115
  BLACK OR AFRICAN AMERICAN                               3                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  61               331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1  58
  1P LOSS WILD-TYPE  10 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   58
  1P LOSS WILD-TYPE   10  346
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              58               346
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    25  22
  1Q LOSS WILD-TYPE 329 223
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47               552 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               223 
$`1Q LOSS MUTATED`
TCGA-L5-A43M TCGA-L5-A4OE TCGA-EQ-A4SO TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IG-A3I8 
        8.94        24.00        16.24         7.63        16.24        33.27 
TCGA-IG-A4QS TCGA-L5-A88V TCGA-LN-A49O TCGA-LN-A5U7 TCGA-LN-A8HZ TCGA-R6-A6DN 
        3.88         2.60        13.41        25.25        12.33         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-V5-A7RE 
        7.59         5.06         6.35         2.89         2.30        16.44 
TCGA-V5-AASX TCGA-VR-A8ER TCGA-XP-A8T8 TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 
        8.98        12.43        14.37         9.44         6.61        17.29 
TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-8289 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-A486 
       19.33        35.24         2.66         1.15        13.02         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-6519 TCGA-D7-A74A 
       11.31        12.43        12.03         4.01        20.55        19.96 
TCGA-HU-8604 TCGA-HU-A4HD TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A93H TCGA-VQ-A8DV 
       22.82        33.40        15.75         2.53        37.64        13.25 
TCGA-VQ-A8PE TCGA-VQ-A925 TCGA-VQ-AA6B TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       22.19         4.54        32.94        12.43         0.79 

$`1Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         4.31         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX 
       20.02        47.05        21.99        22.98        79.07         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       20.15         9.86        27.35        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       14.30        58.55         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
       12.03        12.85        12.26        33.11         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
        7.04        38.40        53.95         9.30        15.78        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        22.82         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 
        3.42         2.10         1.32         2.66        19.73        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4184 
       26.70        11.70        19.56        11.01         9.47         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.87        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.43        12.30        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        11.70        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       46.26        16.31         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       17.13        54.12        26.04        16.14        27.55        17.26 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.79              0.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            37.64            122.30 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            12.43             14.12 
[1] "0.8 - 37.6 (12.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        1        2        2         8         5
  1Q LOSS WILD-TYPE      10       20       45       31        79        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           3          4          7          2        3
  1Q LOSS WILD-TYPE        25         91         65         44       46
                   vv
clus                STAGE IVA
  1Q LOSS MUTATED           1
  1Q LOSS WILD-TYPE         3
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                20
  STAGE IB                 2                45
  STAGE II                 2                31
  STAGE IIA                8                79
  STAGE IIB                5                82
  STAGE III                3                25
  STAGE IIIA               4                91
  STAGE IIIB               7                65
  STAGE IIIC               2                44
  STAGE IV                 3                46
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1Q LOSS MUTATED       3   6  24   7
  1Q LOSS WILD-TYPE    52 130 259 117
D43V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               3                52
  T2                  6               130
  T3                 24               259
  T4                  7               117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q LOSS MUTATED    12  13   9   5
  1Q LOSS WILD-TYPE 195 174  89  91
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              12               195
  N1              13               174
  N2               9                89
  N3               5                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    30   4
  1Q LOSS WILD-TYPE 494  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     30    4
  1Q LOSS WILD-TYPE  494   35
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              30               494
  1               4                35
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    13  34
  1Q LOSS WILD-TYPE 172 406
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     13   34
  1Q LOSS WILD-TYPE  172  406
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              13               172
  MALE                34               406
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    31  10
  1Q LOSS WILD-TYPE 414 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     31   10
  1Q LOSS WILD-TYPE  414  109
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               31               414
  YES              10               109
[1] 2 2
[1] FALSE
D43V9, continuous
D43V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED      10                         1
  1Q LOSS WILD-TYPE   124                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0    30
  1Q LOSS WILD-TYPE                                         1   362
D43V11, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                                  10               124
  BLACK OR AFRICAN AMERICAN                               1                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  30               362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  32
  1Q LOSS WILD-TYPE  10 372
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   32
  1Q LOSS WILD-TYPE   10  372
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              32               372
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    22  12
  2P LOSS WILD-TYPE 332 233
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               34               565 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               12               233 
$`2P LOSS MUTATED`
TCGA-CG-4475 TCGA-VQ-A8PU TCGA-IG-A3YB TCGA-IG-A3YC TCGA-L5-A4OS TCGA-L5-A8NE 
       22.98        27.35         2.63        20.12        58.59        55.50 
TCGA-L5-A8NK TCGA-LN-A49L TCGA-LN-A7HV TCGA-LN-A7HX TCGA-R6-A8W8 TCGA-VR-A8EO 
       13.55        10.45        10.52        12.23         2.89        25.81 
TCGA-VR-A8Q7 TCGA-Z6-AAPN TCGA-BR-6565 TCGA-BR-8060 TCGA-BR-8687 TCGA-CD-8534 
       52.27         2.66         9.17        11.44         8.22        12.07 
TCGA-CD-8535 TCGA-CD-A48A TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 
       12.82        12.43        12.66        20.91        17.19        15.22 
TCGA-D7-8576 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GU TCGA-RD-A7C1 
       14.66        63.06        26.47         5.92         6.58        16.67 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A91Z 
       35.61         5.46        18.48        55.56 

$`2P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        21.99        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF 
       16.24         0.23        20.15         9.86        26.93        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       35.21         0.85        20.78        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       18.31         8.12        28.11        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.10         1.32        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
       12.39        12.59        11.64        15.39        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        10.26        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       77.29        52.21        30.51         1.51        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       63.62        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        5.72        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       18.41        43.66        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.63              0.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            63.06            122.30 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           14.105            13.940 
[1] "2.6 - 63.1 (14.1)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.2"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        0        4        2         7         6
  2P LOSS WILD-TYPE      10       21       43       31        80        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           0         11          1          3        1
  2P LOSS WILD-TYPE        28         84         71         43       48
                   vv
clus                STAGE IVA
  2P LOSS MUTATED           0
  2P LOSS WILD-TYPE         4
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                21
  STAGE IB                 4                43
  STAGE II                 2                31
  STAGE IIA                7                80
  STAGE IIB                6                81
  STAGE III                0                28
  STAGE IIIA              11                84
  STAGE IIIB               1                71
  STAGE IIIC               3                43
  STAGE IV                 1                48
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2P LOSS MUTATED       0  12  18   5
  2P LOSS WILD-TYPE    55 124 265 119
D44V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               0                55
  T2                 12               124
  T3                 18               265
  T4                  5               119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P LOSS MUTATED    13  11   7   4
  2P LOSS WILD-TYPE 194 176  91  92
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              13               194
  N1              11               176
  N2               7                91
  N3               4                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"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    33   0
  2P LOSS WILD-TYPE 491  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     33    0
  2P LOSS WILD-TYPE  491   39
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              33               491
  1               0                39
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    14  22
  2P LOSS WILD-TYPE 171 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     14   22
  2P LOSS WILD-TYPE  171  418
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              14               171
  MALE                22               418
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    24  11
  2P LOSS WILD-TYPE 421 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     24   11
  2P LOSS WILD-TYPE  421  108
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               24               421
  YES              11               108
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED       9                         1
  2P LOSS WILD-TYPE   125                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           0    23
  2P LOSS WILD-TYPE                                         1   369
D44V11, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                                   9               125
  BLACK OR AFRICAN AMERICAN                               1                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  23               369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  24
  2P LOSS WILD-TYPE  11 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   24
  2P LOSS WILD-TYPE   11  380
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              24               380
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    29  17
  2Q LOSS WILD-TYPE 325 228
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               46               553 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17               228 
$`2Q LOSS MUTATED`
TCGA-CG-4475 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       22.98        27.35        26.93         2.63        20.12        18.64 
TCGA-IG-A5B8 TCGA-L5-A43H TCGA-L5-A4OS TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK 
        0.79         0.30        58.59         3.02        16.47        13.55 
TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HX TCGA-R6-A8W8 
       10.45        12.46        12.33        10.52        12.23         2.89 
TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-Z6-AAPN TCGA-BR-6565 TCGA-BR-8687 TCGA-CD-8534 
       25.81        52.27         2.66         9.17         8.22        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4300 TCGA-D7-5578 TCGA-D7-5579 
       12.82         6.31        12.43        20.02        12.66        20.91 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 
       17.19        15.22        14.66        63.06        26.47         5.92 
TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-AB1V TCGA-R5-A7ZE TCGA-RD-A8N9 
       22.75         6.58        33.40        15.75        18.21        35.61 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-AA68 
        5.46        13.02        18.48        43.66 

$`2Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        21.99        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        0.85        20.78         3.88         9.30         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.75        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
        5.92        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30        15.78         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 
       14.37         3.42         2.10         1.32        19.73        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 
       12.39        12.59        11.64        15.39        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 
       69.04        21.07         7.99        25.71        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        10.62        11.70        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        18.41        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              0.3               0.0 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            63.06            122.30 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           14.105            13.940 
[1] "0.3 - 63.1 (14.1)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         1        2        4        2         9         7
  2Q LOSS WILD-TYPE       9       19       43       31        78        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           3         12          2          4        2
  2Q LOSS WILD-TYPE        25         83         70         42       47
                   vv
clus                STAGE IVA
  2Q LOSS MUTATED           0
  2Q LOSS WILD-TYPE         4
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 2                19
  STAGE IB                 4                43
  STAGE II                 2                31
  STAGE IIA                9                78
  STAGE IIB                7                80
  STAGE III                3                25
  STAGE IIIA              12                83
  STAGE IIIB               2                70
  STAGE IIIC               4                42
  STAGE IV                 2                47
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2Q LOSS MUTATED       3  10  27   8
  2Q LOSS WILD-TYPE    52 126 256 116
D45V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               3                52
  T2                 10               126
  T3                 27               256
  T4                  8               116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q LOSS MUTATED    19  14   9   6
  2Q LOSS WILD-TYPE 188 173  89  90
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              19               188
  N1              14               173
  N2               9                89
  N3               6                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    45   1
  2Q LOSS WILD-TYPE 479  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     45    1
  2Q LOSS WILD-TYPE  479   38
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              45               479
  1               1                38
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    14  35
  2Q LOSS WILD-TYPE 171 405
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     14   35
  2Q LOSS WILD-TYPE  171  405
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              14               171
  MALE                35               405
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    31  15
  2Q LOSS WILD-TYPE 414 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     31   15
  2Q LOSS WILD-TYPE  414  104
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               31               414
  YES              15               104
[1] 2 2
[1] FALSE
D45V9, continuous
D45V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED      15                         2
  2Q LOSS WILD-TYPE   119                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           0    27
  2Q LOSS WILD-TYPE                                         1   365
D45V11, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                                  15               119
  BLACK OR AFRICAN AMERICAN                               2                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  27               365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  31
  2Q LOSS WILD-TYPE  11 373
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   31
  2Q LOSS WILD-TYPE   11  373
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              31               373
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   120  64
  3P LOSS WILD-TYPE 234 181
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              184               415 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               64               181 
$`3P LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A8NG TCGA-S8-A6BV TCGA-MX-A663 
       34.85         8.94         4.70        35.97        20.02         9.86 
TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 
       26.93        14.30         5.92        13.94         4.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        3.88         0.53        17.03         0.79        23.41         9.96 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OJ 
       14.50        12.16        68.02        30.25        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.32         7.17         7.13         7.43        15.48         2.60 
TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NS TCGA-LN-A49K 
        7.40         2.66        12.92        13.55        13.41         5.92 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       12.43        12.33        13.15        15.35        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC 
        7.59         7.04         6.35         7.00        20.38         3.42 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       25.81        27.09        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        18.05         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-A5TJ 
       25.08        41.23         3.42         2.10         2.66        11.01 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       17.29        19.33        31.20        35.24        33.63        39.78 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8483 
        9.07        33.21        37.25         0.69         2.66         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A452 
       25.18         9.21        20.22        20.88         8.22         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 
       34.98         1.48        12.89         0.72         0.53        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8526 TCGA-CD-8527 
       20.65        20.42         1.15        21.44        12.53         7.17 
TCGA-CD-8533 TCGA-CD-A48A TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       15.39        12.43        20.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 
        4.01        12.03        18.97        15.02         4.01        12.66 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-A6EX TCGA-EQ-5647 TCGA-EQ-8122 
       13.35        17.19        15.22        11.31         0.62         7.99 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       19.53        14.07        17.06         0.56         5.52         6.21 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4H4 
       18.15        28.96         3.25        22.75         6.58        23.84 
TCGA-IN-7806 TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A93H 
       36.36         6.44        12.59         6.51         5.56        37.64 
TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-RD-A8N6 
       36.95        45.67        18.21         8.52        16.67         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
        5.79        13.25        18.48        37.41        22.19         2.70 
TCGA-VQ-A8PY TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-A94R TCGA-VQ-AA64 
       14.33        42.64         9.50         4.54        42.54        18.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       38.93        32.94        12.43         0.79 

$`3P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI 
       15.68        60.39        18.28         4.31        24.00        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 
       22.82         0.36        27.12         5.16        47.05        21.99 
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       22.98        79.07        16.24         0.23        20.15        27.35 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55         7.63         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       32.45         7.69         9.30        12.82        14.86         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.30        26.33        47.93        18.35         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 
       58.59         4.90        29.00        25.12         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       55.50        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49V 
       10.36        10.45        12.66        13.41        13.38        12.59 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
       13.25        12.59        11.54         7.82         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       16.31        38.40        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        2.30        12.69         5.29        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-AA7B 
        8.98        22.82        12.43         1.55        28.11        11.24 
TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       14.37         1.32        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.87        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 
       18.15        15.32        28.73         3.45        29.56        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 
       14.79         7.36        25.05         3.72         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        31.96        32.58         9.86        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       13.87         6.08        27.55        28.57         8.98        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM 
       28.34         0.66        32.52         0.46        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.10        12.76        12.59        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 
       12.62         3.02        27.02        15.95         1.02        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       29.98        19.07         0.00         9.01         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
        0.99       105.07        12.03        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 
       18.84        18.54        18.61        17.85        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34        19.96         7.13        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27        11.38         3.48        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
       13.58        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.80        21.17        14.07        15.68        33.40         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI TCGA-R5-A7ZR 
       63.62         3.72        19.73        14.04        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        16.87        19.04         0.92        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        43.36        21.73        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       61.22        18.74        20.81        32.88         1.71        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.73        55.56         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA68 
        5.72        66.81        21.04         2.66        11.24        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        17.13        54.12        26.04        16.14        27.55 
TCGA-ZA-A8F6 
       17.26 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.13              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            68.02            122.30 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           12.905            14.790 
[1] "0.1 - 68.0 (12.9)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         4        4       11        7        40        30
  3P LOSS WILD-TYPE       6       17       36       26        47        57
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED          10         30         16         11       14
  3P LOSS WILD-TYPE        18         65         56         35       35
                   vv
clus                STAGE IVA
  3P LOSS MUTATED           1
  3P LOSS WILD-TYPE         3
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  4                 6
  STAGE IA                 4                17
  STAGE IB                11                36
  STAGE II                 7                26
  STAGE IIA               40                47
  STAGE IIB               30                57
  STAGE III               10                18
  STAGE IIIA              30                65
  STAGE IIIB              16                56
  STAGE IIIC              11                35
  STAGE IV                14                35
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3P LOSS MUTATED      19  43  89  31
  3P LOSS WILD-TYPE    36  93 194  93
D46V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              19                36
  T2                 43                93
  T3                 89               194
  T4                 31                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P LOSS MUTATED    72  57  34  17
  3P LOSS WILD-TYPE 135 130  64  79
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              72               135
  N1              57               130
  N2              34                64
  N3              17                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   156  14
  3P LOSS WILD-TYPE 368  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    156   14
  3P LOSS WILD-TYPE  368   25
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             156               368
  1              14                25
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    51 136
  3P LOSS WILD-TYPE 134 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     51  136
  3P LOSS WILD-TYPE  134  304
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              51               134
  MALE               136               304
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   131  40
  3P LOSS WILD-TYPE 314  79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    131   40
  3P LOSS WILD-TYPE  314   79
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO              131               314
  YES              40                79
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED      52                         4
  3P LOSS WILD-TYPE    82                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           0   110
  3P LOSS WILD-TYPE                                         1   282
D46V11, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                                  52                82
  BLACK OR AFRICAN AMERICAN                               4                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 110               282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     3 121
  3P LOSS WILD-TYPE   8 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3  121
  3P LOSS WILD-TYPE    8  283
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO             121               283
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    56  33
  3Q LOSS WILD-TYPE 298 212
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               89               510 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               33               212 
$`3Q LOSS MUTATED`
TCGA-JY-A938 TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM 
       34.85         9.86        26.93        14.30         5.92        13.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YA TCGA-IG-A5S3 TCGA-L5-A43E TCGA-L5-A4OH 
        4.21        32.45        20.78        23.41        30.25        32.61 
TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A8NH TCGA-LN-A49K TCGA-LN-A49P TCGA-LN-A49U 
        7.43         7.40        12.92         5.92        12.33        15.35 
TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX 
       12.46        12.85         4.47        12.33        25.25        12.23 
TCGA-LN-A9FO TCGA-LN-A9FR TCGA-R6-A6XQ TCGA-RE-A7BO TCGA-VR-A8EP TCGA-VR-A8EZ 
        0.13        12.26         6.35         7.00        27.09        18.18 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-A5TJ 
       46.19        18.21        25.08         3.42         2.10        11.01 
TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8058 
       17.29        35.24        33.63        39.78        33.21        37.25 
TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8687 
        0.69         2.66         5.39         9.21        20.22         8.22 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF 
        7.53        34.98        12.89         0.72        13.51         1.15 
TCGA-BR-A4QI TCGA-CD-8526 TCGA-CD-A48A TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 
       21.44        12.53        12.43        54.08         4.01        18.97 
TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-A6EX TCGA-EQ-5647 TCGA-FP-7829 
       15.02        12.66        17.19        11.31         0.62        19.53 
TCGA-FP-8099 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GU TCGA-HU-A4H4 
       17.06         5.52        28.96         3.25         6.58        23.84 
TCGA-IN-7806 TCGA-IN-A6RS TCGA-IN-A7NR TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7O7 
       36.36        12.59         6.51         5.56        37.64        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PY 
       18.21         8.52        13.25        37.41        22.19        14.33 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A94R TCGA-VQ-AA6B TCGA-VQ-AA6K 
       42.64         9.50        42.54        32.94        12.43 

$`3Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH 
       16.24         0.23        20.15        27.35        25.78        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 
       58.55         7.63         8.94        16.24         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.38        13.15        12.59        13.25        12.62 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
       11.54        12.33        13.22        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18        12.03        12.85 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
        1.55        18.31         8.12        28.11        33.70        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 
       18.05        11.24         9.17        15.91        41.23        14.37 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       36.16        35.84        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
        9.07        29.56        14.43        11.44        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56        29.42        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        25.18         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86        20.88        10.68        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08         1.48        27.55        28.57         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        8.05        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         0.56         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.80        21.17        14.07        15.68        33.40         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.44         6.74        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        43.36        21.73        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       13.35        29.59        64.57        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       21.83        61.22        18.74        20.81        32.88         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       60.85         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       11.24        18.41        43.66        28.41        38.93        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        27.55        17.26         0.79 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.13              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            54.08            122.30 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            13.25             14.04 
[1] "0.1 - 54.1 (13.2)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1"  
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        3        3        2        14        20
  3Q LOSS WILD-TYPE       8       18       44       31        73        67
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           3         16         10          5       10
  3Q LOSS WILD-TYPE        25         79         62         41       39
                   vv
clus                STAGE IVA
  3Q LOSS MUTATED           0
  3Q LOSS WILD-TYPE         4
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 3                18
  STAGE IB                 3                44
  STAGE II                 2                31
  STAGE IIA               14                73
  STAGE IIB               20                67
  STAGE III                3                25
  STAGE IIIA              16                79
  STAGE IIIB              10                62
  STAGE IIIC               5                41
  STAGE IV                10                39
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3Q LOSS MUTATED      11  12  46  21
  3Q LOSS WILD-TYPE    44 124 237 103
D47V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1              11                44
  T2                 12               124
  T3                 46               237
  T4                 21               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q LOSS MUTATED    30  29  20  10
  3Q LOSS WILD-TYPE 177 158  78  86
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              30               177
  N1              29               158
  N2              20                78
  N3              10                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    80   9
  3Q LOSS WILD-TYPE 444  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     80    9
  3Q LOSS WILD-TYPE  444   30
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              80               444
  1               9                30
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    26  66
  3Q LOSS WILD-TYPE 159 374
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     26   66
  3Q LOSS WILD-TYPE  159  374
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              26               159
  MALE                66               374
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    71  15
  3Q LOSS WILD-TYPE 374 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     71   15
  3Q LOSS WILD-TYPE  374  104
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               71               374
  YES              15               104
[1] 2 2
[1] FALSE
D47V9, continuous
D47V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED      22                         2
  3Q LOSS WILD-TYPE   112                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           0    57
  3Q LOSS WILD-TYPE                                         1   335
D47V11, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                                  22               112
  BLACK OR AFRICAN AMERICAN                               2                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  57               335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2  60
  3Q LOSS WILD-TYPE   9 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   60
  3Q LOSS WILD-TYPE    9  344
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              60               344
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   153 110
  4P LOSS WILD-TYPE 201 135
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              263               336 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              110               135 
$`4P LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39         8.94        24.00         4.70        35.97        27.12 
TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF 
       47.05        79.07         0.23         9.86        26.93        25.78 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 
       20.12        18.64         3.88         0.53         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93C 
        9.96         4.67        12.16        44.75        47.38        23.18 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
       25.22         3.16        21.01         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.43         7.40         3.75        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.22         5.49         8.71        13.41        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U 
        5.92        10.45        12.66        12.43        13.38        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.25        12.62        12.59        12.49        12.76        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        12.85        12.26         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        7.04         6.35         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ 
       20.38         3.42        16.44         9.27        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.43         1.55         8.12        28.11        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T8 TCGA-Z6-A8JD 
       46.19        18.05        11.24        15.91        14.37         3.42 
TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 
        1.32        58.03        11.01         9.44         6.61         4.08 
TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7197 
        9.67         9.57        17.29         9.17        31.20         9.21 
TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       35.24        18.15        28.73         9.07        33.21        37.25 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.69         9.60         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 
        7.40        31.10        22.19        17.52        14.04        14.79 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 
        3.72         5.39         9.21        20.22        26.73        24.79 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        9.86        10.68         7.53        34.98         1.48         0.72 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 
        0.66        13.51        20.65        21.44        13.02        13.35 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
       11.21        12.59        12.53        12.30        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.07        12.82        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.20        20.02         7.99         8.05        54.08         4.01 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5725 
       19.07        12.03        18.97         7.07        30.97        15.02 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 
       19.13        20.55        17.19        10.26        15.22        11.31 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 
       19.50        18.21        16.44        11.31        19.96         0.62 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF TCGA-HF-7133 
        7.99        11.38        14.07        17.06         5.52        63.06 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        18.15        28.96        22.82 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       22.75        25.81         8.98         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-8663 
       12.95        23.84        21.17        33.40        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.46         6.44         6.74         2.53         5.56        63.62 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS 
       14.04        45.67        18.21         6.08         9.24        11.05 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU 
       16.67        37.91       115.69         8.94        35.61         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 
       13.25        13.02        18.48        43.36        21.73         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS 
       46.26        22.19        12.79         2.70        17.85        13.35 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       73.41        39.45        18.74        42.64         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
       55.56         9.04         4.54        21.04        42.54        11.24 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        16.14        27.55 

$`4P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         4.31        19.99        22.82 
TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO 
        0.36         5.16        20.02        21.99        22.98        16.24 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IG-A3YB 
       20.15        27.35        31.27         7.63         7.69         2.63 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 
        9.30        17.03        23.41        14.86        14.50       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
       68.02         3.68        41.52        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        6.28        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         3.32         7.17         1.38        58.59        29.00 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       15.48         2.60        25.12         3.02        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G 
       13.48         7.76        21.37        83.24        52.57        10.85 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A4 
       13.41        12.33        13.15        12.59        12.46        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HY TCGA-LN-A9FP TCGA-M9-A5M8 
       22.39        11.54         4.47        12.03        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.82        16.31        38.40        53.95         9.30        15.78 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EY 
        5.29        15.35         8.98        25.81        18.31        33.70 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        18.21        25.08        41.23         2.10         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 
       19.73        26.70        11.70        19.56         9.47         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        4.64         7.43        18.35        30.90         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        6.18         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        30.90        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       21.90        36.16        35.84        33.63        39.78        15.32 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 
        3.45        29.56        14.43        11.44        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
        8.05         0.56        29.42         6.18        13.08         0.26 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        7.36        25.05        25.18         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 
        9.34        28.14         6.28         7.53        31.96        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
       20.88         8.22        34.13        13.87         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52         0.46        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8527 
       13.41        13.15        13.18        12.10        12.76         7.17 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG 
       12.33        12.39        12.59        12.43         6.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5717 
       14.01        29.98         0.00         9.01        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 
        7.99        25.71        12.66        20.91        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        13.35        15.98        12.79        12.36 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        8.38         4.34         7.13        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        19.53        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8244 
        0.56         6.21        77.29        52.21        30.51        24.39 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68        24.20         3.25        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.10         6.51        20.25        29.00        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       15.68        36.36         3.45        18.38        13.35        19.53 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64        36.95         3.72        19.73         8.52        74.53 
TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        4.60         8.61         5.13       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       48.79        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       29.59        64.57        14.33        11.70        21.83        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 
       20.81        32.88         1.71        60.85         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 
        6.58         5.72        66.81         2.66        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       28.41        17.13        26.04        12.43        17.26         0.79 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.00 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           115.69            122.30 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           12.850            15.715 
[1] "0.1 - 115.7 (12.8)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         4        4       16       17        45        34
  4P LOSS WILD-TYPE       6       17       31       16        42        53
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED          18         43         32         20       17
  4P LOSS WILD-TYPE        10         52         40         26       32
                   vv
clus                STAGE IVA
  4P LOSS MUTATED           2
  4P LOSS WILD-TYPE         2
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  4                 6
  STAGE IA                 4                17
  STAGE IB                16                31
  STAGE II                17                16
  STAGE IIA               45                42
  STAGE IIB               34                53
  STAGE III               18                10
  STAGE IIIA              43                52
  STAGE IIIB              32                40
  STAGE IIIC              20                26
  STAGE IV                17                32
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4P LOSS MUTATED      18  59 135  47
  4P LOSS WILD-TYPE    37  77 148  77
D48V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              18                37
  T2                 59                77
  T3                135               148
  T4                 47                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P LOSS MUTATED    86  82  48  38
  4P LOSS WILD-TYPE 121 105  50  58
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              86               121
  N1              82               105
  N2              48                50
  N3              38                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   235  13
  4P LOSS WILD-TYPE 289  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    235   13
  4P LOSS WILD-TYPE  289   26
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             235               289
  1              13                26
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    71 203
  4P LOSS WILD-TYPE 114 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     71  203
  4P LOSS WILD-TYPE  114  237
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              71               114
  MALE               203               237
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   189  59
  4P LOSS WILD-TYPE 256  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    189   59
  4P LOSS WILD-TYPE  256   60
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              189               256
  YES              59                60
[1] 2 2
[1] FALSE
D48V9, continuous
D48V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED      71                         7
  4P LOSS WILD-TYPE    63                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           0   158
  4P LOSS WILD-TYPE                                         1   234
D48V11, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                                  71                63
  BLACK OR AFRICAN AMERICAN                               7                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 158               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     4 172
  4P LOSS WILD-TYPE   7 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4  172
  4P LOSS WILD-TYPE    7  232
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 7
  NOT HISPANIC OR LATINO             172               232
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   136 111
  4Q LOSS WILD-TYPE 218 134
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              247               352 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              111               134 
$`4Q LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       60.39         4.31         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U 
       27.12        47.05        79.07         0.23         9.86        26.93 
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 
       20.78         3.88         0.53         0.79        12.82         4.67 
TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OR 
       44.75        47.38        23.18        25.22         3.16         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A891 
        4.90         7.13         7.43        15.48         7.40         3.75 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       12.92        16.47        13.22         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       83.24        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.38        15.35        13.25        12.59        12.76        12.85 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN 
       12.23        13.18        12.33        12.85        12.26         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.59         5.06         7.04        38.40         6.35         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
        2.89         2.30        12.69         7.00        20.38        16.44 
TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
        9.27        27.09        22.82         1.55         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-3M-AB46 
       18.18        52.27        11.24        15.91        25.08        58.03 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 
       11.01         9.44         6.61         4.08         9.67        17.29 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 
       19.33         9.17        31.20        35.24        18.15        28.73 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
        9.07        33.21        37.25        14.43         0.69         9.60 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        2.66        19.96         2.20        15.58         7.40        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 
       22.19        17.52        14.04        14.79         3.72         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 
        9.21        20.22        26.73        24.79         9.86        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
        7.53        34.98         1.48         0.72         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 
       20.65         1.15        21.44        13.02        13.35        11.21 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
       12.59        12.53         7.17        12.30        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.07        12.82        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.20        20.02         7.99         8.05        54.08         4.01 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5730 
       19.07        12.03        18.97        30.97        15.02         4.01 
TCGA-CG-5732 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       69.04        19.13        20.55        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX 
       15.98        11.31        19.50        18.21        16.44        11.31 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 
       19.96         0.62         7.99        11.38        14.07        17.06 
TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 
        5.52        63.06         1.51         5.92        18.15        22.82 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.75         8.98         6.58         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       23.84        21.17        33.40        18.81         3.39        12.46 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A666 TCGA-R5-A7O7 
        6.44         6.74        10.62         2.53        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW 
       18.21         6.08         9.24        11.05        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
      115.69         8.94        35.61         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       18.48        43.36        21.73         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91A 
       12.79         2.70        17.85        13.35        73.41        39.45 
TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       18.74         9.50         9.73        55.56         9.04         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       21.04        42.54        32.94        54.12        16.14        27.55 
TCGA-VQ-AA6K 
       12.43 

$`4Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        34.85        18.28        19.99        22.82         0.36 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-KB-A93G 
        5.16        20.02        21.99        22.98        16.24        20.15 
TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A3YC 
       27.35        31.27         7.63         7.69         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
       18.64         9.30        17.03        23.41         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16       122.10        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       21.70        31.56        24.03         6.28        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88W 
        7.17         1.38        58.59        29.00         2.60        25.12 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM 
        3.02        55.50         2.66        13.48        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       21.37        52.57        10.85        12.43        13.41        12.33 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 
       13.15        12.59        12.62        12.46        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A7HY TCGA-LN-A8I0 
       22.39        15.52        11.54        13.22        12.03        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
       13.18         0.13        12.03        33.11         7.82        16.31 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX 
       53.95        15.78         5.29         3.42        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G 
       25.81        12.43        18.31        33.70        46.19        18.05 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        18.21        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       15.95        13.87        13.68        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8060 
       33.63        39.78        15.32         3.45        29.56        11.44 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8360 
       29.59        32.25         8.05         0.56        29.42         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       13.08         0.26         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8487 
       11.80        31.27         7.36        25.05        25.18         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        32.58        20.88         8.22        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL 
        0.53        28.34        32.52         0.46        20.42        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 
        5.13        13.41        13.15        13.18        12.10        12.76 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG 
       12.33        12.39        12.59        12.43         6.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       14.01        29.98         0.00         9.01         7.07        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
      105.07        12.03        28.96        65.10        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       25.71        12.66        20.91        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       17.85        13.35        12.79        12.36        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        17.19        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.13        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM 
       22.29        59.54         5.03        13.58         0.56         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 
       77.29        52.21        30.51        26.47        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 
       29.98         0.10         6.51        20.25        29.00        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL 
       14.07        15.68        36.36         3.45        18.38        13.35 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53        12.59         6.51        11.70        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        8.52        74.53         4.60         8.61         5.13       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA 
       40.64       116.38        71.38        57.44        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79         0.92        48.79        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO 
       30.97        34.29        16.31         2.50         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D 
       23.41        15.65        29.59        64.57        14.33        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       60.85         2.01        55.43         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        17.26         0.79 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.23              0.00 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           115.69            122.30 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            12.85             15.65 
[1] "0.2 - 115.7 (12.8)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.4"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         3        4       15       16        35        33
  4Q LOSS WILD-TYPE       7       17       32       17        52        54
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED          18         37         32         20       19
  4Q LOSS WILD-TYPE        10         58         40         26       30
                   vv
clus                STAGE IVA
  4Q LOSS MUTATED           2
  4Q LOSS WILD-TYPE         2
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  3                 7
  STAGE IA                 4                17
  STAGE IB                15                32
  STAGE II                16                17
  STAGE IIA               35                52
  STAGE IIB               33                54
  STAGE III               18                10
  STAGE IIIA              37                58
  STAGE IIIB              32                40
  STAGE IIIC              20                26
  STAGE IV                19                30
  STAGE IVA                2                 2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4Q LOSS MUTATED      14  53 125  48
  4Q LOSS WILD-TYPE    41  83 158  76
D49V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              14                41
  T2                 53                83
  T3                125               158
  T4                 48                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q LOSS MUTATED    74  79  45  38
  4Q LOSS WILD-TYPE 133 108  53  58
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              74               133
  N1              79               108
  N2              45                53
  N3              38                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   214  15
  4Q LOSS WILD-TYPE 310  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    214   15
  4Q LOSS WILD-TYPE  310   24
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             214               310
  1              15                24
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    70 186
  4Q LOSS WILD-TYPE 115 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     70  186
  4Q LOSS WILD-TYPE  115  254
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              70               115
  MALE               186               254
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   183  48
  4Q LOSS WILD-TYPE 262  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    183   48
  4Q LOSS WILD-TYPE  262   71
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              183               262
  YES              48                71
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED      63                         6
  4Q LOSS WILD-TYPE    71                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           0   153
  4Q LOSS WILD-TYPE                                         1   239
D49V11, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                                  63                71
  BLACK OR AFRICAN AMERICAN                               6                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 153               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     5 158
  4Q LOSS WILD-TYPE   6 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5  158
  4Q LOSS WILD-TYPE    6  246
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 6
  NOT HISPANIC OR LATINO             158               246
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    57  52
  5P LOSS WILD-TYPE 297 193
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              109               490 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               52               193 
$`5P LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-MX-A663 
       60.39        24.00         4.70        27.12        20.02         9.86 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3QL 
       58.55         7.63        13.94         8.94         4.21        35.21 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-L5-A43E 
        3.88         0.53        17.03         4.67       122.10        30.25 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OS TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
       26.33        21.01        58.59         2.60         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NR TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49V 
        2.66         5.49         8.71         5.92        10.45        12.59 
TCGA-LN-A4A8 TCGA-LN-A7HV TCGA-LN-A8I0 TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6XG 
       15.52        10.52        13.38        12.26        33.11        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-AASW 
        6.35         9.30         2.89         2.30        12.69         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-AA4D TCGA-X8-AAAR TCGA-B7-A5TJ 
        8.98        22.82        12.43        46.19        18.21        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7958 
        9.44         6.61         9.67        19.33         9.17        29.56 
TCGA-BR-7959 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8683 TCGA-BR-8690 
       33.21         2.20        14.04         5.39         9.86        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PE TCGA-BR-A4QI 
        7.53        34.98         1.48         0.72        20.42        21.44 
TCGA-CD-5800 TCGA-CD-8527 TCGA-CD-8535 TCGA-CD-A4MH TCGA-CG-4440 TCGA-CG-4449 
       13.15         7.17        12.82        12.20         4.01        19.07 
TCGA-D7-6520 TCGA-D7-6815 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF 
       18.84        15.98         7.99        72.23         0.56         5.52 
TCGA-FP-A9TM TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
        6.21         5.92         0.76        11.77         8.98         6.58 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL 
       12.95        23.84        21.17        36.36        18.81        13.35 
TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A8MW TCGA-SW-A7EB 
        6.44        63.62         8.52         6.08        37.91         5.79 
TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PS 
       13.02         7.73        22.19        12.79         2.70        13.35 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R 
        1.71        42.64         9.73         9.04        21.04        42.54 
TCGA-ZQ-A9CR 
        0.79 

$`5P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        34.85        18.28         4.31         8.94        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 
       22.82         0.36        35.97         5.16        47.05        21.99 
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       22.98        79.07        16.24         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO 
       26.93        25.78        31.27        14.30         5.92        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
       20.12        18.64         9.30         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH 
       25.22        24.03         6.28         3.16         0.30        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W 
        4.90        29.00         7.13         7.43        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40        55.50        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         7.76        21.37        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.85        10.36        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        12.03        12.85         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 
        7.59         5.06        16.31         7.04        53.95        15.78 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       25.81        27.09         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        32.58        20.88         8.22        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65         1.15        16.14         5.13        13.41        13.02 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       54.08        14.01        29.98        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62        14.47        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 
       20.25         0.26         2.10        29.00        23.80        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       15.68        33.40         3.45         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67        18.21        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87        19.04         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.25        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       21.83        61.22        18.74        20.81        32.88        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.50        55.56         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        5.72        66.81         2.66        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.53              0.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            122.1             122.3 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           11.010            14.825 
[1] "0.5 - 122.1 (11.0)" "0.0 - 122.3 (14.8)"
[1] "hr=" "1.5"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         7        3        2        3        13        18
  5P LOSS WILD-TYPE       3       18       45       30        74        69
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           9         18         11          6        5
  5P LOSS WILD-TYPE        19         77         61         40       44
                   vv
clus                STAGE IVA
  5P LOSS MUTATED           1
  5P LOSS WILD-TYPE         3
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  7                 3
  STAGE IA                 3                18
  STAGE IB                 2                45
  STAGE II                 3                30
  STAGE IIA               13                74
  STAGE IIB               18                69
  STAGE III                9                19
  STAGE IIIA              18                77
  STAGE IIIB              11                61
  STAGE IIIC               6                40
  STAGE IV                 5                44
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5P LOSS MUTATED      18  17  44  21
  5P LOSS WILD-TYPE    37 119 239 103
D50V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              18                37
  T2                 17               119
  T3                 44               239
  T4                 21               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P LOSS MUTATED    29  40  16  13
  5P LOSS WILD-TYPE 178 147  82  83
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              29               178
  N1              40               147
  N2              16                82
  N3              13                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    89   5
  5P LOSS WILD-TYPE 435  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     89    5
  5P LOSS WILD-TYPE  435   34
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              89               435
  1               5                34
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    27  83
  5P LOSS WILD-TYPE 158 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     27   83
  5P LOSS WILD-TYPE  158  357
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              27               158
  MALE                83               357
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    82  19
  5P LOSS WILD-TYPE 363 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     82   19
  5P LOSS WILD-TYPE  363  100
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               82               363
  YES              19               100
[1] 2 2
[1] FALSE
D50V9, continuous
D50V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED      25                         5
  5P LOSS WILD-TYPE   109                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           0    66
  5P LOSS WILD-TYPE                                         1   326
D50V11, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                                  25               109
  BLACK OR AFRICAN AMERICAN                               5                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  66               326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     2  69
  5P LOSS WILD-TYPE   9 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   69
  5P LOSS WILD-TYPE    9  335
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              69               335
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   108  85
  5Q LOSS WILD-TYPE 246 160
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              193               406 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               85               160 
$`5Q LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39        24.00         4.70         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GJ 
        5.16        20.02        47.05         9.86        27.35        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63        13.94         8.94        16.24         4.21        32.45 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       35.21         2.63        20.12        18.64         3.88         0.53 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93D TCGA-L5-A43E 
        4.67        14.50       122.10        47.38        31.56        30.25 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       26.33        21.01        47.93         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        4.90         7.13         2.60         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
        2.66        13.55         5.49         8.71        13.41        52.57 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49U TCGA-LN-A4A2 
       10.85         5.92        10.45        12.43        15.35        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HZ 
       22.39        15.52        12.33        12.33        10.52        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       12.33        13.38        13.18        12.85        12.26        33.11 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       38.40         6.35         9.30         2.89         2.30        12.69 
TCGA-S8-A6BW TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       20.38         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR 
       12.43         8.12        28.11        52.27        46.19        18.21 
TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-A5TJ TCGA-B7-A5TN 
       25.08         2.10         1.32         2.66        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 
        6.61         9.67        19.33         9.17         9.21        35.24 
TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8289 
       39.78         3.45        29.56        33.21        29.42         2.66 
TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8678 TCGA-BR-8683 
        2.20        14.04        14.79         5.39        24.79         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        8.22        10.68         7.53        34.98         1.48         0.72 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8526 
       20.42        21.44        13.15        13.18        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48C 
        7.17        12.33        15.39        12.82        11.31        11.61 
TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-5718 
       12.20        27.02        54.08         4.01        19.07        36.00 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 
       20.91        18.84        10.26        15.98        12.79        12.33 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF 
       11.31        22.29         7.99        72.23         0.56         5.52 
TCGA-FP-A9TM TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        6.21         5.92         0.76         3.25        22.75        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD 
        8.98         6.58        12.95        23.84        21.17        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-AB1V TCGA-KB-A6F7 
       36.36        18.81        13.35         6.44        15.75        63.62 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N6 
       18.21         8.52         6.08         8.61        37.91         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 
        5.79         5.46        13.25        13.02        43.36         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS 
       46.26        22.19        12.79         2.70        17.85        13.35 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        1.71        42.64         9.73        55.56         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D 
        4.54        21.04        42.54        43.66        38.93        17.13 
TCGA-ZQ-A9CR 
        0.79 

$`5Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        34.85        18.28         4.31         8.94        19.99 
TCGA-L5-A88T TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       22.82        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL 
       20.15        26.93        25.78        31.27        14.30         5.92 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A51D 
        7.69        33.27         0.85        20.78         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I 
        0.79        23.41        12.82         9.96        14.86        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH 
       25.22        24.03         6.28         3.16         0.30        32.61 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
       18.35         3.32         1.38        29.00         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       25.12         7.40        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M 
        7.76        21.37        83.24        46.09        10.36        12.66 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        13.15        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.62        12.46        12.59        12.76        12.59        12.85 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       11.54        13.22         4.47        25.25        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-LN-A9FP TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03         0.13        12.03         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO 
        5.06        16.31         7.04        53.95        15.78         7.00 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-A8EU 
        5.29         3.42        16.44        15.35         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        18.18        18.05        11.24         9.17        15.91 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 
       41.23        14.37         3.42        19.73        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.70        19.56         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       44.94        21.90        36.16        35.84        33.63        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
       15.32        28.73         9.07        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       19.96        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
       32.58        20.88        34.13        13.87         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.66        32.52        13.51         0.46        20.65         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 
       16.14         5.13        13.41        13.02        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.10        12.76        12.30        12.39        12.59        11.64 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG 
       12.07        12.43         6.31        12.30        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 
        7.99         8.05        14.01        29.98        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        7.99        25.71        12.66        19.13        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 
       18.61        17.85        13.35        17.19        15.22        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62        14.47        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF 
       24.30         5.59        24.26        22.68        24.20        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
        2.10        29.00        23.80        14.07        15.68         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39        18.38        12.46        19.53         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        11.70        13.51         2.53         5.56 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       74.53         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E0 
       35.61        16.87        19.04         0.92        48.79        18.48 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       21.83        61.22        18.74        20.81        32.88        60.85 
TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        9.50        55.43         6.58         5.72        66.81         2.66 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       11.24        18.41        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.36              0.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            122.1             122.3 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            12.79             15.12 
[1] "0.4 - 122.1 (12.8)" "0.0 - 122.3 (15.1)"
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         7        7        8        9        26        29
  5Q LOSS WILD-TYPE       3       14       39       24        61        58
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED          11         42         17         11        9
  5Q LOSS WILD-TYPE        17         53         55         35       40
                   vv
clus                STAGE IVA
  5Q LOSS MUTATED           3
  5Q LOSS WILD-TYPE         1
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  7                 3
  STAGE IA                 7                14
  STAGE IB                 8                39
  STAGE II                 9                24
  STAGE IIA               26                61
  STAGE IIB               29                58
  STAGE III               11                17
  STAGE IIIA              42                53
  STAGE IIIB              17                55
  STAGE IIIC              11                35
  STAGE IV                 9                40
  STAGE IVA                3                 1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5Q LOSS MUTATED      23  40  89  32
  5Q LOSS WILD-TYPE    32  96 194  92
D51V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              23                32
  T2                 40                96
  T3                 89               194
  T4                 32                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q LOSS MUTATED    58  71  31  21
  5Q LOSS WILD-TYPE 149 116  67  75
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              58               149
  N1              71               116
  N2              31                67
  N3              21                75
[1] 4 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   164   9
  5Q LOSS WILD-TYPE 360  30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    164    9
  5Q LOSS WILD-TYPE  360   30
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0             164               360
  1               9                30
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    51 144
  5Q LOSS WILD-TYPE 134 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     51  144
  5Q LOSS WILD-TYPE  134  296
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              51               134
  MALE               144               296
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   141  39
  5Q LOSS WILD-TYPE 304  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    141   39
  5Q LOSS WILD-TYPE  304   80
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO              141               304
  YES              39                80
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED      47                         7
  5Q LOSS WILD-TYPE    87                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           1   117
  5Q LOSS WILD-TYPE                                         0   275
D51V11, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                                  47                87
  BLACK OR AFRICAN AMERICAN                               7                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 117               275
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     3 117
  5Q LOSS WILD-TYPE   8 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3  117
  5Q LOSS WILD-TYPE    8  287
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO             117               287
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    56  34
  6P LOSS WILD-TYPE 298 211
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               90               509 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               34               211 
$`6P LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88Y TCGA-S8-A6BV 
       60.39         4.31         8.94         4.70         0.36        20.02 
TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L 
       16.24         9.86        27.35        33.27        35.21         0.53 
TCGA-IG-A5S3 TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A4OR TCGA-L5-A8NJ TCGA-L5-A8NK 
       23.41        23.18         3.16         3.16        16.47        13.55 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49W 
       83.24        52.57         5.92        12.43        13.41        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.59        12.49        25.25        13.18        12.33        13.38 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER 
        2.30        12.69         3.42         9.27        22.82        12.43 
TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        8.12        18.18        25.08         3.42         2.66        19.73 
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7716 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 
        6.18        17.29        39.78        34.98         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A48A 
       20.65         1.15        12.39        11.64        12.82        12.43 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 
        1.02        12.03        15.02        12.66        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-F1-A72C 
       18.54        13.35        15.98        11.31        15.65        11.38 
TCGA-FP-8099 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 
       17.06        26.47        22.75        11.77         6.58        12.95 
TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-R5-A7ZR 
       33.40        13.35         6.44        10.62        11.70         6.08 
TCGA-RD-A7C1 TCGA-RD-A8N5 TCGA-VQ-A8DU TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A922 
       16.67        57.44         5.46        14.33        20.81         9.04 
TCGA-VQ-A925 TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.54        54.12        16.14        27.55        17.26         0.79 

$`6P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28        24.00        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       35.97        27.12         5.16        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       79.07         0.23        20.15        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         4.21        32.45         7.69         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       13.41        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV 
       11.54        12.33        13.22         4.47        12.33        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.00        12.23        12.03        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30        15.78         2.89         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET 
       16.44        15.35         8.98        25.81        27.09         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31        28.11        33.70        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        41.23        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        33.63        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
       28.34         0.66        32.52         0.46        20.42        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 
        7.17        12.33        12.30        12.59        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        12.30        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        25.71        20.91 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       19.13        18.61        17.85        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       26.43        11.24        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51        20.25         0.26         2.10        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       18.81         3.39        18.38        12.46        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         6.51        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       63.62        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       23.41        15.65        13.35        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.01        55.43         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K 
       38.93        32.94        17.13        26.04        12.43 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.36              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            83.24            122.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           13.215            14.270 
[1] "0.4 - 83.2 (13.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         2        2        6        2        18        13
  6P LOSS WILD-TYPE       8       19       41       31        69        74
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           5         15         10          4        4
  6P LOSS WILD-TYPE        23         80         62         42       45
                   vv
clus                STAGE IVA
  6P LOSS MUTATED           0
  6P LOSS WILD-TYPE         4
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 2                19
  STAGE IB                 6                41
  STAGE II                 2                31
  STAGE IIA               18                69
  STAGE IIB               13                74
  STAGE III                5                23
  STAGE IIIA              15                80
  STAGE IIIB              10                62
  STAGE IIIC               4                42
  STAGE IV                 4                45
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6P LOSS MUTATED       6  21  49  11
  6P LOSS WILD-TYPE    49 115 234 113
D52V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               6                49
  T2                 21               115
  T3                 49               234
  T4                 11               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P LOSS MUTATED    36  24  15  10
  6P LOSS WILD-TYPE 171 163  83  86
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              36               171
  N1              24               163
  N2              15                83
  N3              10                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    74   2
  6P LOSS WILD-TYPE 450  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     74    2
  6P LOSS WILD-TYPE  450   37
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              74               450
  1               2                37
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    21  72
  6P LOSS WILD-TYPE 164 368
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21   72
  6P LOSS WILD-TYPE  164  368
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              21               164
  MALE                72               368
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    64  18
  6P LOSS WILD-TYPE 381 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     64   18
  6P LOSS WILD-TYPE  381  101
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               64               381
  YES              18               101
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED      24                         4
  6P LOSS WILD-TYPE   110                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           0    58
  6P LOSS WILD-TYPE                                         1   334
D52V11, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                                  24               110
  BLACK OR AFRICAN AMERICAN                               4                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  58               334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2  62
  6P LOSS WILD-TYPE   9 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   62
  6P LOSS WILD-TYPE    9  342
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              62               342
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    63  45
  6Q LOSS WILD-TYPE 291 200
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              108               491 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               45               200 
$`6Q LOSS MUTATED`
TCGA-L5-A43M TCGA-L5-A88Y TCGA-S8-A6BV TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU 
        8.94         0.36        20.02        16.24         9.86        27.35 
TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FH 
       25.78        33.27        35.21         4.67        14.50        47.38 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OR TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NS 
       25.22         3.16         3.16        16.47        13.55        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49W 
       83.24        52.57         5.92        12.43        13.41        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A8HZ 
       12.59        12.49        22.39        13.22        25.25        12.33 
TCGA-R6-A6XG TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW 
       38.40         2.30        12.69        20.38         3.42         9.27 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-XP-A8T6 
       22.82        12.43         8.12        28.11        18.18        25.08 
TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7716 
        3.42        19.73         6.18        17.29         9.17        39.78 
TCGA-BR-7722 TCGA-BR-8080 TCGA-BR-A4CQ TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
       15.32         9.60        34.98        13.51        20.65         1.15 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A48A 
       11.21        12.10        12.39        11.64        12.82        12.43 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 
       29.98        12.03         1.02        12.03        15.02        12.66 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-8570 
       20.55        18.84        18.54        13.35        15.98        24.72 
TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 
       14.66        11.31        15.65        19.96        11.38        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4H4 
       13.58         0.56        26.47        22.75         6.58        23.84 
TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A93J 
       33.40        13.35         6.44        10.62        11.70        36.95 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-VQ-A8DU 
       18.21         6.08        16.67       122.30        57.44         5.46 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 
       13.35        14.33        20.81         9.04         2.01         4.54 
TCGA-VQ-A94O TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.04        54.12        16.14        27.55        17.26         0.79 

$`6Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       26.93        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
        3.68        41.52        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.48        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        8.71        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.46        12.76        12.59        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.33         4.47        12.33        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       15.78         2.89         7.00         5.29        16.44        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
        8.98        25.81        27.09         1.55        18.31        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.21        41.23        14.37         2.10         1.32         2.66 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         9.67         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       37.25        14.43        11.44         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18        13.35        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 
        7.17        12.33        12.30        12.59        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        12.30        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       14.01        19.07         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       12.00        30.97         6.97        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99       105.07        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
       21.07         7.99        25.71        20.91        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       17.85        17.19        10.26        15.22        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       22.29         8.38         4.34         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       22.29        59.54         5.03         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       18.81         3.39        18.38        12.46        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         6.51        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        37.64         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        9.73        55.56        55.43         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K 
       38.93        32.94        17.13        26.04        12.43 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.36              0.00 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            122.3             122.1 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           13.565            14.010 
[1] "0.4 - 122.3 (13.6)" "0.0 - 122.1 (14.0)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         0        2        7        5        18        17
  6Q LOSS WILD-TYPE      10       19       40       28        69        70
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           6         19         12          7        4
  6Q LOSS WILD-TYPE        22         76         60         39       45
                   vv
clus                STAGE IVA
  6Q LOSS MUTATED           1
  6Q LOSS WILD-TYPE         3
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 2                19
  STAGE IB                 7                40
  STAGE II                 5                28
  STAGE IIA               18                69
  STAGE IIB               17                70
  STAGE III                6                22
  STAGE IIIA              19                76
  STAGE IIIB              12                60
  STAGE IIIC               7                39
  STAGE IV                 4                45
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6Q LOSS MUTATED       5  26  60  14
  6Q LOSS WILD-TYPE    50 110 223 110
D53V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1               5                50
  T2                 26               110
  T3                 60               223
  T4                 14               110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q LOSS MUTATED    35  33  20  14
  6Q LOSS WILD-TYPE 172 154  78  82
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              35               172
  N1              33               154
  N2              20                78
  N3              14                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"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    89   3
  6Q LOSS WILD-TYPE 435  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     89    3
  6Q LOSS WILD-TYPE  435   36
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              89               435
  1               3                36
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    24  88
  6Q LOSS WILD-TYPE 161 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     24   88
  6Q LOSS WILD-TYPE  161  352
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              24               161
  MALE                88               352
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    77  22
  6Q LOSS WILD-TYPE 368  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     77   22
  6Q LOSS WILD-TYPE  368   97
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               77               368
  YES              22                97
[1] 2 2
[1] FALSE
D53V9, continuous
D53V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED      24                         5
  6Q LOSS WILD-TYPE   110                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           0    71
  6Q LOSS WILD-TYPE                                         1   321
D53V11, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                                  24               110
  BLACK OR AFRICAN AMERICAN                               5                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  71               321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     2  73
  6Q LOSS WILD-TYPE   9 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   73
  6Q LOSS WILD-TYPE    9  331
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              73               331
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    21  12
  7P LOSS WILD-TYPE 333 233
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               33               566 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               12               233 
$`7P LOSS MUTATED`
TCGA-Q9-A6FU TCGA-2H-A9GI TCGA-IG-A3Y9 TCGA-JY-A6FD TCGA-L5-A4OM TCGA-L5-A4OU 
        5.16        14.30         0.85        68.02        47.93        29.00 
TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NS TCGA-LN-A49L TCGA-LN-A4A8 TCGA-LN-A7HY 
       55.50        13.48        13.41        10.45        15.52        12.03 
TCGA-BR-4255 TCGA-BR-7723 TCGA-BR-8678 TCGA-CD-8528 TCGA-CG-4438 TCGA-CG-4443 
        4.08        28.73        24.79        12.33        54.08        29.98 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A6EX TCGA-FP-8631 TCGA-HU-A4GH TCGA-HU-A4GU 
       11.31        19.50        11.31         0.56        11.77         6.58 
TCGA-HU-A4H6 TCGA-IN-A6RN TCGA-IN-A7NU TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU 
       21.17        19.53        11.70        37.91        35.61         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8PJ TCGA-VQ-A91S 
       18.48         2.70        32.88 

$`7P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       16.24         0.23        20.15         9.86        27.35        26.93 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        32.61        21.01        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        12.85        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.66        19.73        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        12.36        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       13.58         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       30.51        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        13.35         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
        2.53         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79        13.25        13.02        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31        22.19         2.50        12.79        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        20.81         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.56              0.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            68.02            122.30 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           14.300            13.905 
[1] "0.6 - 68.0 (14.3)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0        3        1        1         6         4
  7P LOSS WILD-TYPE      10       18       46       32        81        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           3          8          5          0        2
  7P LOSS WILD-TYPE        25         87         67         46       47
                   vv
clus                STAGE IVA
  7P LOSS MUTATED           0
  7P LOSS WILD-TYPE         4
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 3                18
  STAGE IB                 1                46
  STAGE II                 1                32
  STAGE IIA                6                81
  STAGE IIB                4                83
  STAGE III                3                25
  STAGE IIIA               8                87
  STAGE IIIB               5                67
  STAGE IIIC               0                46
  STAGE IV                 2                47
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7P LOSS MUTATED       4   6  18   5
  7P LOSS WILD-TYPE    51 130 265 119
D54V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               4                51
  T2                  6               130
  T3                 18               265
  T4                  5               119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P LOSS MUTATED    12   9  10   2
  7P LOSS WILD-TYPE 195 178  88  94
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              12               195
  N1               9               178
  N2              10                88
  N3               2                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    30   1
  7P LOSS WILD-TYPE 494  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     30    1
  7P LOSS WILD-TYPE  494   38
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              30               494
  1               1                38
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     9  24
  7P LOSS WILD-TYPE 176 416
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      9   24
  7P LOSS WILD-TYPE  176  416
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               9               176
  MALE                24               416
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    23   7
  7P LOSS WILD-TYPE 422 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     23    7
  7P LOSS WILD-TYPE  422  112
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               23               422
  YES               7               112
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED       9                         2
  7P LOSS WILD-TYPE   125                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           0    18
  7P LOSS WILD-TYPE                                         1   374
D54V11, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                                   9               125
  BLACK OR AFRICAN AMERICAN                               2                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  18               374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  20
  7P LOSS WILD-TYPE  11 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   20
  7P LOSS WILD-TYPE   11  384
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              20               384
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    31  18
  7Q LOSS WILD-TYPE 323 227
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               49               550 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               18               227 
$`7Q LOSS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A5B8 TCGA-JY-A6FD 
       14.30         5.92         0.85        20.12         0.79        68.02 
TCGA-L5-A4OU TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NS 
       29.00        55.50        13.48        13.55         8.71        13.41 
TCGA-LN-A49L TCGA-LN-A49X TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-V5-AASX 
       10.45        12.62        12.03        33.11         5.06         8.98 
TCGA-VR-A8ET TCGA-VR-AA7I TCGA-BR-4255 TCGA-BR-7723 TCGA-BR-8369 TCGA-BR-8678 
        1.55        15.91         4.08        28.73        14.04        24.79 
TCGA-BR-A4CS TCGA-CD-8528 TCGA-CD-A48C TCGA-CG-4438 TCGA-CG-4443 TCGA-D7-6815 
        1.48        12.33        11.61        54.08        29.98        15.98 
TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EX TCGA-FP-7829 TCGA-FP-8631 TCGA-HU-A4GD 
       11.31        18.21        11.31        19.53         0.56        22.75 
TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN 
       11.77         6.58        21.17        33.40        18.38        19.53 
TCGA-IN-A7NU TCGA-KB-A93H TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8E0 
       11.70        37.64        37.91        35.61         5.46        18.48 
TCGA-VQ-A8PJ 
        2.70 

$`7Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       79.07        16.24         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       26.93        25.78        31.27        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       35.21        20.78         2.63        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE 
        4.67        14.50        12.16       122.10        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        2.66        12.92        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       21.37        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
        5.92        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        12.26         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU 
        9.27        25.81        27.09        22.82        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
       35.84        33.63        39.78        18.15        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        34.98        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        8.05         4.01        14.01        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       17.19        10.26        15.22        12.79        12.36        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ 
       24.26        22.68        24.20         3.25        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       15.68        36.36         3.45        18.81         3.39        12.46 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        48.79        13.25        13.02        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK 
       46.26        16.31        22.19         2.50        12.79        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       38.93        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.56              0.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            68.02            122.30 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           13.550            13.975 
[1] "0.6 - 68.0 (13.6)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         1        2        2        1         9         9
  7Q LOSS WILD-TYPE       9       19       45       32        78        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           6         11          4          1        2
  7Q LOSS WILD-TYPE        22         84         68         45       47
                   vv
clus                STAGE IVA
  7Q LOSS MUTATED           0
  7Q LOSS WILD-TYPE         4
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 2                19
  STAGE IB                 2                45
  STAGE II                 1                32
  STAGE IIA                9                78
  STAGE IIB                9                78
  STAGE III                6                22
  STAGE IIIA              11                84
  STAGE IIIB               4                68
  STAGE IIIC               1                45
  STAGE IV                 2                47
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7Q LOSS MUTATED       4   7  31   6
  7Q LOSS WILD-TYPE    51 129 252 118
D55V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               4                51
  T2                  7               129
  T3                 31               252
  T4                  6               118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q LOSS MUTATED    17  15  12   4
  7Q LOSS WILD-TYPE 190 172  86  92
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              17               190
  N1              15               172
  N2              12                86
  N3               4                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"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    46   1
  7Q LOSS WILD-TYPE 478  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     46    1
  7Q LOSS WILD-TYPE  478   38
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              46               478
  1               1                38
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    13  37
  7Q LOSS WILD-TYPE 172 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     13   37
  7Q LOSS WILD-TYPE  172  403
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              13               172
  MALE                37               403
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    36   8
  7Q LOSS WILD-TYPE 409 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     36    8
  7Q LOSS WILD-TYPE  409  111
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               36               409
  YES               8               111
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED      13                         1
  7Q LOSS WILD-TYPE   121                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           0    29
  7Q LOSS WILD-TYPE                                         1   363
D55V11, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                                  13               121
  BLACK OR AFRICAN AMERICAN                               1                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  29               363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  32
  7Q LOSS WILD-TYPE  11 372
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   32
  7Q LOSS WILD-TYPE   11  372
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              32               372
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    91  60
  8P LOSS WILD-TYPE 263 185
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              151               448 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               60               185 
$`8P LOSS MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A8NT TCGA-Q9-A6FU 
       60.39        34.85         8.94        24.00        27.12         5.16 
TCGA-CG-4444 TCGA-CG-4475 TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RE 
       47.05        22.98        25.78         5.92        13.94         7.69 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
        0.85         2.63        20.12         3.88         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93C TCGA-JY-A93E 
       23.41         9.96        14.50        44.75        23.18        25.22 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A88Z TCGA-L5-A891 
       26.33        32.61        21.01         3.32         7.40         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L5-A8NR TCGA-LN-A49L TCGA-LN-A49M 
       55.50         2.66         5.49         8.71        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MQ 
       12.43        12.46        12.59        12.49        22.39        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.22        12.33        12.00        13.18        12.85        12.26 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        7.82         8.02         2.30        20.38         5.29         3.42 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       12.43        18.31        52.27        18.05         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TN 
       25.08        41.23         2.66        58.03        19.56         9.44 
TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-7716 
       18.35        17.29         9.17        25.61        12.16        39.78 
TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8362 
       28.73        29.56         0.69        29.42        15.58        13.08 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4IY 
       31.96        32.58         9.86         8.22        13.87        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8526 TCGA-CD-8533 
        0.72        13.51         1.15        21.44        12.53        15.39 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       11.61        12.20         3.02         7.99        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 
       29.98        19.07        12.03         4.01        69.04        12.66 
TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-A4YU 
       18.54        10.26        15.22        24.72        18.21        16.44 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-8245 
       15.65        19.96         0.62        17.06         5.92        18.15 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-A6RP TCGA-IN-A6RR 
       28.96         0.76         6.58        33.40         6.44         6.74 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A666 
       11.70        15.75         2.53         5.56        36.95        14.04 
TCGA-R5-A7O7 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-VQ-A8E0 
       45.67         9.24         8.61       122.30        37.91        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS 
       43.36        37.41        46.26        17.85         1.87        13.35 
TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94T 
       14.33        20.81         1.71        55.56         4.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       18.41        43.66        32.94        54.12        16.14        27.55 
TCGA-VQ-AA6K 
       12.43 

$`8P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        18.28         4.31         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO 
        0.36        35.97        20.02        21.99        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH 
        0.23        20.15         9.86        27.35        26.93        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30        58.55         7.63         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT 
       32.45        33.27        35.21        20.78        18.64         9.30 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       17.03        12.82        14.86         4.67        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D 
       68.02         3.68        41.52        47.38        21.70        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OM 
       24.03         6.28         3.16        30.25         0.30        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76        21.37        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.85        10.36         5.92        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 
       13.15        15.35        12.59        13.25        12.62        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59        12.85        15.52        11.54         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.13        12.03        33.11         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        2.89        12.69         7.00        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW 
        8.98        25.81        27.09        22.82         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR 
       28.11        33.70        18.18        46.19        11.24        18.21 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         2.10         1.32        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.70        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 
       13.68        19.33        39.12        26.10        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       18.15        15.32         3.45         9.07        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
        0.56         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 
        6.28         7.53        26.73        24.79        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       28.57         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52         0.46        20.65        20.42        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.10        12.76        12.59         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        11.64        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI 
        6.31        12.30        11.31        12.43         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       12.62        20.02        27.02        15.95         1.02         8.05 
TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       14.01        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       18.84        18.61        17.85        13.35        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44        20.32        22.29         8.38         4.34         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       30.51        26.47         1.51        24.39        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       12.46        13.35        19.53        12.59         6.51        10.62 
TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE 
       13.51        63.62        37.64         3.72        19.73        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52        74.53         6.08         4.60        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       16.67        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       48.79         5.46        13.25        13.02        21.73        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       37.22         7.73        30.97        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        12.79         2.70         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        32.88        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        21.04         2.66        42.54        28.41        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        17.26         0.79 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.53              0.00 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            122.3             122.1 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           13.870            14.025 
[1] "0.5 - 122.3 (13.9)" "0.0 - 122.1 (14.0)"
[1] "hr=" "1"  
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         4        4        6        5        19        23
  8P LOSS WILD-TYPE       6       17       41       28        68        64
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           7         24         29         11       14
  8P LOSS WILD-TYPE        21         71         43         35       35
                   vv
clus                STAGE IVA
  8P LOSS MUTATED           1
  8P LOSS WILD-TYPE         3
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  4                 6
  STAGE IA                 4                17
  STAGE IB                 6                41
  STAGE II                 5                28
  STAGE IIA               19                68
  STAGE IIB               23                64
  STAGE III                7                21
  STAGE IIIA              24                71
  STAGE IIIB              29                43
  STAGE IIIC              11                35
  STAGE IV                14                35
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8P LOSS MUTATED      16  29  81  26
  8P LOSS WILD-TYPE    39 107 202  98
D56V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              16                39
  T2                 29               107
  T3                 81               202
  T4                 26                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P LOSS MUTATED    41  49  33  26
  8P LOSS WILD-TYPE 166 138  65  70
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              41               166
  N1              49               138
  N2              33                65
  N3              26                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   133  10
  8P LOSS WILD-TYPE 391  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    133   10
  8P LOSS WILD-TYPE  391   29
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             133               391
  1              10                29
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    31 125
  8P LOSS WILD-TYPE 154 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     31  125
  8P LOSS WILD-TYPE  154  315
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              31               154
  MALE               125               315
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   109  31
  8P LOSS WILD-TYPE 336  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    109   31
  8P LOSS WILD-TYPE  336   88
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              109               336
  YES              31                88
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED      36                         5
  8P LOSS WILD-TYPE    98                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           1    91
  8P LOSS WILD-TYPE                                         0   301
D56V11, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                                  36                98
  BLACK OR AFRICAN AMERICAN                               5                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  91               301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     5  90
  8P LOSS WILD-TYPE   6 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5   90
  8P LOSS WILD-TYPE    6  314
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 6
  NOT HISPANIC OR LATINO              90               314
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    35  23
  8Q LOSS WILD-TYPE 319 222
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               58               541 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               23               222 
$`8Q LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-CG-4444 TCGA-CG-4475 TCGA-2H-A9GL TCGA-IG-A5S3 
       60.39         8.94        47.05        22.98         5.92        23.41 
TCGA-JY-A6FA TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A891 
       44.75        25.22        26.33        32.61        21.01         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49Y TCGA-LN-A4MQ 
       55.50         2.66        10.45        12.43        12.46        12.33 
TCGA-LN-A4MR TCGA-LN-A7HW TCGA-V5-A7RC TCGA-VR-A8Q7 TCGA-XP-A8T6 TCGA-B7-A5TN 
       13.22        12.00         3.42        52.27        25.08         9.44 
TCGA-BR-4191 TCGA-BR-6705 TCGA-BR-8286 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-A48C 
       18.35        25.61        29.42        13.51        21.44        11.61 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-5724 TCGA-D7-6521 
       12.20         7.99         4.01        29.98        12.03        18.54 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 TCGA-FP-8099 TCGA-HU-8249 TCGA-HU-A4GU 
       10.26        15.22        24.72        17.06        28.96         6.58 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-VQ-A8E0 
       11.70        15.75         9.24         8.61       122.30        18.48 
TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A91U TCGA-VQ-A925 
       37.41        17.85         1.87        14.33         1.71         4.54 
TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J 
       11.24        32.94        54.12        27.55 

$`8Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       20.02        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
        9.86        27.35        26.93        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16       122.10        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        3.16        30.25         0.30        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       52.57        46.09        10.85        10.36         5.92        12.66 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 
       22.39        12.85        15.52        11.54         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
       12.43         6.31        12.30        11.31        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 
        1.02         8.05        54.08        14.01        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       30.51        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       74.53         6.08         4.60        11.05         5.13        16.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.25        13.02        43.36        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       16.31        22.19         2.50        12.79         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       23.41        15.65        13.35        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       39.45        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       32.88        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        9.04         2.01        55.43         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       21.04         2.66        42.54        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       38.93        17.13        26.04        16.14        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.71              0.00 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            122.3             122.1 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           15.485            13.870 
[1] "1.7 - 122.3 (15.5)" "0.0 - 122.1 (13.9)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         3        2        2        2         7        11
  8Q LOSS WILD-TYPE       7       19       45       31        80        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           2          7         11          0        5
  8Q LOSS WILD-TYPE        26         88         61         46       44
                   vv
clus                STAGE IVA
  8Q LOSS MUTATED           1
  8Q LOSS WILD-TYPE         3
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  3                 7
  STAGE IA                 2                19
  STAGE IB                 2                45
  STAGE II                 2                31
  STAGE IIA                7                80
  STAGE IIB               11                76
  STAGE III                2                26
  STAGE IIIA               7                88
  STAGE IIIB              11                61
  STAGE IIIC               0                46
  STAGE IV                 5                44
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8Q LOSS MUTATED       7  13  34   3
  8Q LOSS WILD-TYPE    48 123 249 121
D57V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               7                48
  T2                 13               123
  T3                 34               249
  T4                  3               121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q LOSS MUTATED    17  18  12   9
  8Q LOSS WILD-TYPE 190 169  86  87
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              17               190
  N1              18               169
  N2              12                86
  N3               9                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    51   4
  8Q LOSS WILD-TYPE 473  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     51    4
  8Q LOSS WILD-TYPE  473   35
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              51               473
  1               4                35
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    11  48
  8Q LOSS WILD-TYPE 174 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     11   48
  8Q LOSS WILD-TYPE  174  392
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              11               174
  MALE                48               392
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    44  10
  8Q LOSS WILD-TYPE 401 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     44   10
  8Q LOSS WILD-TYPE  401  109
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               44               401
  YES              10               109
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED      12                         4
  8Q LOSS WILD-TYPE   122                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           1    33
  8Q LOSS WILD-TYPE                                         0   359
D57V11, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                                  12               122
  BLACK OR AFRICAN AMERICAN                               4                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  33               359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  29
  8Q LOSS WILD-TYPE  10 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   29
  8Q LOSS WILD-TYPE   10  375
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              29               375
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   143  99
  9P LOSS WILD-TYPE 211 146
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              242               357 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               99               146 
$`9P LOSS MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A8NG TCGA-Q9-A6FU 
       60.39        34.85        18.28         8.94        35.97         5.16 
TCGA-S8-A6BV TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       20.02        27.35        26.93        25.78        31.27        14.30 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A4P3 
        8.94        16.24         4.21         7.69        20.78        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 
        3.88         0.53         0.79        23.41         9.96         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH 
       14.50        12.16        25.22         3.16        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
       47.93        18.35         7.17        58.59         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ 
       15.48         2.60         3.75        55.50         2.66        16.47 
TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
       13.22         8.71        13.41        83.24        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.43        13.15        15.35        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        22.39        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        12.03        13.18        12.33         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
       12.26        33.11         5.06        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       15.78         2.30        12.69         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55        18.31         8.12        28.11        52.27        46.19 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-3M-AB46 
       18.21        41.23        14.37         3.42        19.73        58.03 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6457 
       11.01         9.44        18.35         4.08         9.67        13.68 
TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7717 
       19.33        31.20         9.21        35.24        39.78        18.15 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8291 
       28.73         3.45        37.25        11.44         0.69        19.96 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       22.19        17.52        14.04         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ 
       20.22         9.86        20.88         8.22        13.87        34.98 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
        1.48         0.72         0.66        13.51        20.65         1.15 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.02        13.15        11.21        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A48C 
        7.17        11.64        15.39        12.07         6.31        11.61 
TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        3.02        54.08         4.01        29.98        19.07        12.03 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5730 
       18.97        12.00        36.00         1.02        15.02         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       69.04        12.66        20.91        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8576 
       13.35        17.19        10.26        15.98        12.79        14.66 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A 
       21.14        16.44        11.24        11.31        22.29        19.96 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A9TM 
        7.99        72.23        11.38        17.06         0.56         6.21 
TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GU 
       63.06         1.51         5.92        18.15        11.77         6.58 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RR 
       21.17        33.40        36.36        18.81        12.46         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 
        6.51        10.62        15.75        37.64        36.95        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW 
       45.67         8.52         6.08         9.24         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 
       16.67        37.91         8.94         5.79        13.25        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       43.36        37.41         7.73        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q 
       17.85         1.87        64.57        14.33        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-A94R 
        1.71        42.64         9.50         9.73        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J 
       11.24        18.41        43.66        38.93        54.12        27.55 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`9P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68         4.31        24.00         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        0.36        27.12        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GJ TCGA-2H-A9GK 
       16.24         0.23        20.15         9.86        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        5.92        13.94        32.45        33.27        35.21         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP 
        2.63        20.12         9.30        17.03        12.82        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        23.18        31.56        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
        0.30        21.01         3.32         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
       29.00        25.12         7.40         3.02        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW 
       13.55         7.76         5.49        21.37        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.85        10.36         5.92        13.41        12.33        13.38 
TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.59        12.59        11.54         4.47        13.38        13.18 
TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.85         7.82         8.02         7.59        16.31         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EY 
       53.95         2.89         7.00        20.38        15.35        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       18.18        18.05        11.24         9.17        15.91        25.08 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.47         6.61         6.97         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.87        17.29        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       40.21        30.90        44.94        21.90        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       33.63        15.32         9.07        29.56        33.21        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       13.08         0.26         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8690 
        7.53        26.73        24.79        31.96        32.58        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       34.13         7.53         6.08        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
        8.98        14.17         0.53        28.34        32.52         0.46 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
       20.42        21.44        16.14         5.13        13.41        13.18 
TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       13.35        12.10        12.33        12.30        12.39        12.59 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
       12.82        12.43        12.30        11.31        12.43         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        12.62        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4462 TCGA-CG-4465 
        1.02         7.99         8.05        14.01         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        7.07        30.97         6.97         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
      105.07        12.03        28.96        65.10        21.07         7.99 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 
       25.71        19.13        18.61        17.85        15.22        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       18.21        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       14.76        26.43        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        4.34         7.13         0.62        14.47        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
        5.52        77.29        52.21        30.51        26.47        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       23.80        14.07        15.68         3.45         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1X 
       13.35        19.53         6.44        12.59        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE 
        2.53         5.56        63.62         3.72        19.73        18.21 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
       74.53         4.60        11.05       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92        48.79         5.46        13.02        21.73        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       37.22        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ 
        9.27        23.41        15.65        13.35        29.59        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W 
       39.45        11.70        21.83        61.22        32.88        60.85 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        5.72        66.81         2.66        28.41        32.94        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        17.26 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              0.00 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            83.24            122.30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            13.22             14.76 
[1] "0.1 - 83.2 (13.2)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         2       10       13       16        37        38
  9P LOSS WILD-TYPE       8       11       34       17        50        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED          16         31         27         13       19
  9P LOSS WILD-TYPE        12         64         45         33       30
                   vv
clus                STAGE IVA
  9P LOSS MUTATED           4
  9P LOSS WILD-TYPE         0
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                10                11
  STAGE IB                13                34
  STAGE II                16                17
  STAGE IIA               37                50
  STAGE IIB               38                49
  STAGE III               16                12
  STAGE IIIA              31                64
  STAGE IIIB              27                45
  STAGE IIIC              13                33
  STAGE IV                19                30
  STAGE IVA                4                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9P LOSS MUTATED      24  59 114  38
  9P LOSS WILD-TYPE    31  77 169  86
D58V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              24                31
  T2                 59                77
  T3                114               169
  T4                 38                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P LOSS MUTATED    78  83  42  29
  9P LOSS WILD-TYPE 129 104  56  67
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              78               129
  N1              83               104
  N2              42                56
  N3              29                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   206  14
  9P LOSS WILD-TYPE 318  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    206   14
  9P LOSS WILD-TYPE  318   25
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             206               318
  1              14                25
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    66 183
  9P LOSS WILD-TYPE 119 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     66  183
  9P LOSS WILD-TYPE  119  257
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              66               119
  MALE               183               257
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   170  55
  9P LOSS WILD-TYPE 275  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    170   55
  9P LOSS WILD-TYPE  275   64
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              170               275
  YES              55                64
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED      58                         8
  9P LOSS WILD-TYPE    76                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           1   147
  9P LOSS WILD-TYPE                                         0   245
D58V11, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                                  58                76
  BLACK OR AFRICAN AMERICAN                               8                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 147               245
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     7 152
  9P LOSS WILD-TYPE   4 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7  152
  9P LOSS WILD-TYPE    4  252
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                 4
  NOT HISPANIC OR LATINO             152               252
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    94  73
  9Q LOSS WILD-TYPE 260 172
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              167               432 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               73               172 
$`9Q LOSS MUTATED`
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A8NG TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       18.28         8.94        35.97        26.93        25.78        31.27 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS 
       16.24         4.21         0.85        20.78        18.64         3.88 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A93E 
        0.79        23.41         9.96         4.67        14.50        25.22 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       26.33        47.93        58.59         7.13        15.48         2.60 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L 
       55.50         2.66        13.22        13.41        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.66        12.43        13.15        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.76        12.85        12.33        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-R6-A6KZ 
       12.03        13.18        12.33        13.18         0.13         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-V5-A7RB 
       38.40         6.35         9.30        15.78        12.69         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW 
        3.42        16.44        25.81        27.09         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T8 
       28.11        52.27        46.19        11.24        18.21        14.37 
TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6457 
        3.42        19.73        11.01         4.08         9.67        13.68 
TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 
       19.33        31.20         9.21        39.78        28.73         3.45 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8483 
       37.25        11.44        19.96        22.19        17.52         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8686 TCGA-BR-A44U TCGA-BR-A4CS TCGA-BR-A4J1 
       25.18         9.21        20.88        13.87         1.48         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.51         1.15        13.02        11.21        12.76        12.59 
TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A48C 
        7.17        11.64        15.39        12.07         6.31        11.61 
TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4455 
       12.20         3.02        54.08         4.01        29.98        12.03 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
       20.55        18.84        18.54        13.35        10.26        15.98 
TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6F0 
       12.79        18.21        14.66        21.14        16.44        22.29 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 
       19.96         7.99        72.23        11.38        17.06        13.58 
TCGA-FP-8631 TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 
        0.56        63.06         5.92        11.77         6.58         2.10 
TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V 
       33.40        18.38        12.46         6.74         6.51        15.75 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR 
       37.64        36.95        14.04        45.67         8.52         6.08 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 
       16.67        37.91         8.94         5.79        13.25        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       43.36        37.41        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A94O 
       13.35        64.57        20.81         1.71         9.73        21.04 
TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J 
       42.54        43.66        38.93        54.12        27.55 

$`9Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82         0.36        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.15         9.86        27.35        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        5.92        13.94         8.94        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       35.21         2.63        20.12         9.30         0.53        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       12.82        14.86        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25         0.30        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        4.90        29.00         7.43        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        3.02        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        5.49        21.37         8.71        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U 
       10.36         5.92        13.41        12.33        13.38        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        13.25        12.62        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A8I0 
       11.54        12.33        13.22         4.47        25.25        13.38 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.59        16.31         7.04        53.95         2.89         2.30 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
        7.00        20.38        15.35         9.27         8.98        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7D 
       12.43        18.31        33.70        18.18        18.05         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       15.91        25.08        41.23         2.10         1.32         2.66 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.87        17.29        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       40.21        30.90        44.94        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 
       35.84        33.63        18.15        15.32         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       33.21        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 
        7.40         6.18        31.10        13.08         0.26         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 
       14.79         7.36        25.05         3.72        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
       26.73        24.79        31.96        32.58         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       10.68        34.13         7.53         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
        0.66        32.52         0.46        20.65        20.42        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       16.14         5.13        13.41        13.15        13.18        13.35 
TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.10        12.53        12.33        12.30        12.39        12.59 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
       12.82        12.43        12.30        11.31        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 
        7.99         8.05        14.01        19.07         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
        7.99        25.71        12.66        20.91        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        17.19        15.22        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT 
       24.72        16.80        19.50        17.19        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.13         0.62        14.47        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM 
       14.07        22.29        59.54         5.03         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       77.29        52.21        30.51        26.47         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51        20.25         0.26        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
       18.81         3.39        13.35        19.53         6.44        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        11.70        13.51         2.53         5.56        63.62 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73        18.21        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         8.61         5.13       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92        48.79         5.46        13.02        21.73        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z 
       18.74        32.88        42.64        60.85         9.50        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
       66.81         2.66        11.24        18.41        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        16.14        12.43        17.26         0.79 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.13              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            83.24            122.30 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           13.250            14.315 
[1] "0.1 - 83.2 (13.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         1        7        9       12        26        28
  9Q LOSS WILD-TYPE       9       14       38       21        61        59
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           8         23         18         11       11
  9Q LOSS WILD-TYPE        20         72         54         35       38
                   vv
clus                STAGE IVA
  9Q LOSS MUTATED           4
  9Q LOSS WILD-TYPE         0
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 7                14
  STAGE IB                 9                38
  STAGE II                12                21
  STAGE IIA               26                61
  STAGE IIB               28                59
  STAGE III                8                20
  STAGE IIIA              23                72
  STAGE IIIB              18                54
  STAGE IIIC              11                35
  STAGE IV                11                38
  STAGE IVA                4                 0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9Q LOSS MUTATED      16  41  82  25
  9Q LOSS WILD-TYPE    39  95 201  99
D59V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              16                39
  T2                 41                95
  T3                 82               201
  T4                 25                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q LOSS MUTATED    55  55  27  24
  9Q LOSS WILD-TYPE 152 132  71  72
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              55               152
  N1              55               132
  N2              27                71
  N3              24                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   140  12
  9Q LOSS WILD-TYPE 384  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    140   12
  9Q LOSS WILD-TYPE  384   27
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             140               384
  1              12                27
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    41 132
  9Q LOSS WILD-TYPE 144 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     41  132
  9Q LOSS WILD-TYPE  144  308
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              41               144
  MALE               132               308
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   121  38
  9Q LOSS WILD-TYPE 324  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    121   38
  9Q LOSS WILD-TYPE  324   81
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              121               324
  YES              38                81
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED      43                         8
  9Q LOSS WILD-TYPE    91                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           0   103
  9Q LOSS WILD-TYPE                                         1   289
D59V11, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                                  43                91
  BLACK OR AFRICAN AMERICAN                               8                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 103               289
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     5 111
  9Q LOSS WILD-TYPE   6 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5  111
  9Q LOSS WILD-TYPE    6  293
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 6
  NOT HISPANIC OR LATINO             111               293
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    62  52
  10P LOSS WILD-TYPE 292 193
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               114                485 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                52                193 
$`10P LOSS MUTATED`
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-CG-4475 
        4.31         8.94        24.00         4.70        27.12        22.98 
TCGA-FP-A8CX TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 
        0.23        25.78        14.30         5.92        33.27         0.85 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43H 
        0.53         0.79        23.41        14.50        23.18         0.30 
TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NU 
        3.32         4.90         7.13        13.55        13.41        83.24 
TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       10.85        12.66        13.41        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
        4.47        25.25        12.00        13.18        12.33        13.38 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-V5-A7RC TCGA-V5-A7RE 
        0.13        12.85        12.26         7.82         3.42        16.44 
TCGA-VR-A8EP TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
       27.09         8.12        28.11        18.18        18.05        11.24 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-BR-4191 
       25.08        14.37         3.42         2.66        19.56        18.35 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7704 TCGA-BR-7901 
        9.67         6.18        19.33        26.10        35.24         3.45 
TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-A452 
       11.44        19.96        17.52        25.18        20.22         7.53 
TCGA-BR-A4IY TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 TCGA-CG-4436 
       12.89        12.59         7.17        12.33        15.39         7.99 
TCGA-CG-4455 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       12.03        69.04        18.54        10.26        15.22        15.98 
TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EV TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8631 
       11.31        18.21        11.24         7.99        19.53         0.56 
TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8249 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RP 
        5.52        63.06        28.96        18.81        18.38         6.44 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A8N1 TCGA-RD-A8N6 
        6.74         6.51        45.67         8.52       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE 
        5.79        48.79        13.02        18.48        43.36        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A928 
       17.85        13.35        39.45        18.74        20.81         5.72 
TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       21.04        11.24        18.41        43.66        16.14         0.79 

$`10P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39        34.85        18.28        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 
        0.36        35.97         5.16        20.02        47.05        21.99 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07        16.24        20.15         9.86        27.35        26.93 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        32.45         7.69        35.21        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 
       20.12        18.64         3.88         9.30        17.03        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D 
       68.02         3.68        41.52        47.38        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16        58.59        29.00         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       21.37         8.71        52.57        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.43        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U6 
       12.76        12.59        22.39        12.85        15.52        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 
       10.52        12.23        12.03        13.18        12.03        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
       12.69         7.00        20.38         5.29        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        22.82        12.43         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       33.70        52.27        46.19         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 
       41.23         2.10         1.32        19.73        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       32.25         8.05         0.56        29.42         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39         9.21         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        19.07         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        20.91        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       17.85        13.35        17.19        12.79        12.36        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM 
       22.29        17.06        59.54         5.03        13.58         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ 
       15.68        33.40        36.36         3.45         3.39        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
       13.35        19.53        12.59        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73        14.04        18.21        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61        16.87        19.04         0.92         5.46        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        46.26        16.31         2.50        12.79         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       14.33        73.41        11.70        21.83        61.22        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.04         2.01        55.43         4.54         6.58        66.81 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
        2.66        42.54        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        27.55        12.43        17.26 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.13               0.00 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            115.69             122.30 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            13.285             14.070 
[1] "0.1 - 115.7 (13.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         2        2        5        5        17        21
  10P LOSS WILD-TYPE       8       19       42       28        70        66
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           5         17         14          9       12
  10P LOSS WILD-TYPE        23         78         58         37       37
                    vv
clus                 STAGE IVA
  10P LOSS MUTATED           1
  10P LOSS WILD-TYPE         3
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  2                 19
  STAGE IB                  5                 42
  STAGE II                  5                 28
  STAGE IIA                17                 70
  STAGE IIB                21                 66
  STAGE III                 5                 23
  STAGE IIIA               17                 78
  STAGE IIIB               14                 58
  STAGE IIIC                9                 37
  STAGE IV                 12                 37
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10P LOSS MUTATED       8  29  61  14
  10P LOSS WILD-TYPE    47 107 222 110
D60V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1                8                 47
  T2                  29                107
  T3                  61                222
  T4                  14                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P LOSS MUTATED    35  32  23  22
  10P LOSS WILD-TYPE 172 155  75  74
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               35                172
  N1               32                155
  N2               23                 75
  N3               22                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   101   8
  10P LOSS WILD-TYPE 423  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    101    8
  10P LOSS WILD-TYPE  423   31
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0              101                423
  1                8                 31
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    30  88
  10P LOSS WILD-TYPE 155 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     30   88
  10P LOSS WILD-TYPE  155  352
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               30                155
  MALE                 88                352
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    82  26
  10P LOSS WILD-TYPE 363  93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     82   26
  10P LOSS WILD-TYPE  363   93
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                82                363
  YES               26                 93
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED      27                         8
  10P LOSS WILD-TYPE   107                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           0    68
  10P LOSS WILD-TYPE                                         1   324
D60V11, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                                   27                107
  BLACK OR AFRICAN AMERICAN                                8                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   68                324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     3  72
  10P LOSS WILD-TYPE   8 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3   72
  10P LOSS WILD-TYPE    8  332
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               72                332
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    70  44
  10Q LOSS WILD-TYPE 284 201
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               114                485 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                44                201 
$`10Q LOSS MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4475 TCGA-FP-A8CX 
       24.00         4.70        27.12         5.16        22.98         0.23 
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB 
       25.78        14.30         5.92        33.27         0.85         2.63 
TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H 
        0.53        23.41        14.50        23.18         3.16         0.30 
TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NK TCGA-L5-A8NU TCGA-L7-A56G 
        3.32         4.90         7.13        13.55        83.24        10.85 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.66        13.38        12.46        12.49        22.39        12.85 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        12.33        13.22        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-V5-A7RC 
       12.03        13.18        13.38        13.18        12.26         3.42 
TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-XP-A8T6 TCGA-XP-A8T8 
       16.44        27.09        28.11        18.18        25.08        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4257 
        2.10         1.32         2.66        19.56        18.35         9.67 
TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 
       19.33        35.24         3.45        11.44        19.96        17.52 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4CQ 
        5.39        25.18         9.21        20.22         9.86        34.98 
TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-4440 
       13.02        12.59        12.33        12.43         7.99         4.01 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 
       12.03        18.97         4.01        19.13        18.54        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8631 
       15.22        15.98        12.79         7.99        19.53         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4HD 
        5.52         5.92        28.96        22.82        11.77        33.40 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H 
       18.81        18.38         6.44         6.74         6.51        37.64 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
       45.67         8.52         8.94         5.79        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91N 
       13.02        18.48        22.19        17.85        39.45        18.74 
TCGA-VQ-A91X TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
        9.50        21.04        11.24        43.66        38.93         0.79 

$`10Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV TCGA-CG-4444 
       19.99        22.82         0.36        35.97        20.02        47.05 
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       21.99        79.07        16.24        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       26.93        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA 
       16.24         4.21        32.45         7.69        35.21        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF 
       31.56        25.22        24.03         6.28        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16        58.59        29.00         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37         8.71        13.41        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
        5.92        10.45        12.43        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 
       15.35        12.59        13.25        12.62        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A8HZ 
       12.59        15.52         4.47        10.52        12.23        12.33 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.38         5.29        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-3M-AB46 
       15.91        18.21        41.23         3.42        19.73        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       31.10        13.08         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        7.36        25.05         3.72         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        32.52        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        1.15        21.44        16.14         5.13        13.41        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       14.01        29.98        19.07         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.91        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       17.19        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM 
       22.29        17.06        59.54         5.03        13.58         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        18.15        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
        3.45         3.39        12.46        13.35        19.53        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE 
       63.62        36.95         3.72        19.73        14.04        18.21 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        13.25        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        21.83        61.22        20.81        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       42.64        60.85         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        66.81         2.66 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       42.54        18.41        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.23               0.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             83.24             122.30 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            12.935             14.330 
[1] "0.2 - 83.2 (12.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         2        3        4        5        19        17
  10Q LOSS WILD-TYPE       8       18       43       28        68        70
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           7         21         11         12        8
  10Q LOSS WILD-TYPE        21         74         61         34       41
                    vv
clus                 STAGE IVA
  10Q LOSS MUTATED           1
  10Q LOSS WILD-TYPE         3
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  3                 18
  STAGE IB                  4                 43
  STAGE II                  5                 28
  STAGE IIA                19                 68
  STAGE IIB                17                 70
  STAGE III                 7                 21
  STAGE IIIA               21                 74
  STAGE IIIB               11                 61
  STAGE IIIC               12                 34
  STAGE IV                  8                 41
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10Q LOSS MUTATED       9  29  56  17
  10Q LOSS WILD-TYPE    46 107 227 107
D61V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1                9                 46
  T2                  29                107
  T3                  56                227
  T4                  17                107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q LOSS MUTATED    33  37  19  22
  10Q LOSS WILD-TYPE 174 150  79  74
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               33                174
  N1               37                150
  N2               19                 79
  N3               22                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   102   8
  10Q LOSS WILD-TYPE 422  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    102    8
  10Q LOSS WILD-TYPE  422   31
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              102                422
  1                8                 31
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    31  87
  10Q LOSS WILD-TYPE 154 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     31   87
  10Q LOSS WILD-TYPE  154  353
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               31                154
  MALE                 87                353
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    81  26
  10Q LOSS WILD-TYPE 364  93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     81   26
  10Q LOSS WILD-TYPE  364   93
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                81                364
  YES               26                 93
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED      32                         8
  10Q LOSS WILD-TYPE   102                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           0    64
  10Q LOSS WILD-TYPE                                         1   328
D61V11, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                                   32                102
  BLACK OR AFRICAN AMERICAN                                8                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   64                328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3  78
  10Q LOSS WILD-TYPE   8 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3   78
  10Q LOSS WILD-TYPE    8  326
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               78                326
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    68  48
  11P LOSS WILD-TYPE 286 197
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               116                483 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                48                197 
$`11P LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4460 
       34.85         4.70         0.36        27.12        47.05        21.99 
TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3Y9 
       27.35        31.27        14.30         5.92         4.21         0.85 
TCGA-IG-A3YB TCGA-IG-A5S3 TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A4OP 
        2.63        23.41         3.16         0.30         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.16         2.60         3.02        55.50        16.47        13.55 
TCGA-L5-A8NL TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       13.22        10.85        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.41        13.38        13.25        12.59        12.49        12.76 
TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       12.85        12.33        12.03        13.18         0.13        12.85 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        5.06        38.40         6.35         2.89         2.30        12.69 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8ER TCGA-VR-A8EX TCGA-XP-A8T6 TCGA-XP-A8T8 
       16.44         9.27        12.43        28.11        25.08        14.37 
TCGA-Z6-A8JE TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7723 
        2.10         6.61         6.97         9.57        26.10        28.73 
TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-CD-5799 
        9.60         2.66         7.40         1.48         0.72        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4443 
       13.15        13.35         7.17         6.31        12.43        29.98 
TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       30.97        12.03         4.01        12.66        20.91        20.55 
TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8578 TCGA-D7-A74A 
       18.54        10.26        15.22        15.98        21.14        19.96 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8211 TCGA-HJ-7597 TCGA-HU-8245 
        0.62        72.23        11.38        13.58        26.47        18.15 
TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
       28.96        22.75         2.10        23.84        23.80        21.17 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-R5-A7O7 TCGA-R5-A7ZE 
        3.39        13.35         6.44         6.74        45.67        18.21 
TCGA-RD-A8MW TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS 
       37.91        48.79        13.25        37.41        17.85        13.35 
TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
       18.74        55.56         9.04         4.54        21.04        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6K 
       43.66        12.43 

$`11P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4475 
       19.99        22.82        35.97         5.16        20.02        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U 
       79.07        16.24         0.23        20.15         9.86        26.93 
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
       32.45         7.69        33.27        35.21        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NH 
       15.48        25.12         7.40         3.75         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49P TCGA-LN-A49S 
       83.24        52.57        46.09         5.92        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
       15.35        12.59        12.62        12.46        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO 
       16.31         7.04        53.95         9.30        15.78         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
       20.38         5.29         3.42        15.35         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       27.09        22.82         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       15.91        18.21        41.23         3.42         1.32         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       19.73        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         9.44         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 
        4.08         4.08         9.34         9.67         6.18         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56        29.42        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       15.58         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       12.07        12.82        12.43        12.30        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        12.00         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 
       65.10        69.04        21.07         7.99        25.71        19.13 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 
       18.84        18.61        17.85        13.35        17.19        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        14.66        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        4.34         7.13         7.99        14.47        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       30.51         1.51         5.92        24.39        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.95        29.00        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS 
        3.45        18.81        18.38        12.46        19.53        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       14.04         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       16.87        19.04         5.79         0.92         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        43.36        21.73        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       60.85         9.50         9.73         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
        5.72        66.81         2.66        11.24        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       38.93        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        17.26         0.79 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.13               0.00 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             72.23             122.30 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            12.935             14.760 
[1] "0.1 - 72.2 (12.9)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         2        4        7        7        13        14
  11P LOSS WILD-TYPE       8       17       40       26        74        73
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED          12         20          4         10        9
  11P LOSS WILD-TYPE        16         75         68         36       40
                    vv
clus                 STAGE IVA
  11P LOSS MUTATED           1
  11P LOSS WILD-TYPE         3
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  4                 17
  STAGE IB                  7                 40
  STAGE II                  7                 26
  STAGE IIA                13                 74
  STAGE IIB                14                 73
  STAGE III                12                 16
  STAGE IIIA               20                 75
  STAGE IIIB                4                 68
  STAGE IIIC               10                 36
  STAGE IV                  9                 40
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11P LOSS MUTATED      11  29  51  17
  11P LOSS WILD-TYPE    44 107 232 107
D62V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               11                 44
  T2                  29                107
  T3                  51                232
  T4                  17                107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P LOSS MUTATED    34  41  15  17
  11P LOSS WILD-TYPE 173 146  83  79
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               34                173
  N1               41                146
  N2               15                 83
  N3               17                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    92   8
  11P LOSS WILD-TYPE 432  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     92    8
  11P LOSS WILD-TYPE  432   31
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               92                432
  1                8                 31
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    27  90
  11P LOSS WILD-TYPE 158 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     27   90
  11P LOSS WILD-TYPE  158  350
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               27                158
  MALE                 90                350
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    76  31
  11P LOSS WILD-TYPE 369  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     76   31
  11P LOSS WILD-TYPE  369   88
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                76                369
  YES               31                 88
[1] 2 2
[1] FALSE
D62V9, continuous
D62V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED      30                         5
  11P LOSS WILD-TYPE   104                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           0    67
  11P LOSS WILD-TYPE                                         1   325
D62V11, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                                   30                104
  BLACK OR AFRICAN AMERICAN                                5                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   67                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4  71
  11P LOSS WILD-TYPE   7 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4   71
  11P LOSS WILD-TYPE    7  333
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               71                333
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    69  52
  11Q LOSS WILD-TYPE 285 193
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               121                478 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                52                193 
$`11Q LOSS MUTATED`
TCGA-L5-A4OG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-2H-A9GL 
        4.70        27.12        20.02         0.23        27.35         5.92 
TCGA-2H-A9GQ TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97I 
        4.21        20.12        18.64        23.41         9.96        12.16 
TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
       47.38         3.16         0.30        47.93         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        3.16        15.48         2.60         3.02        55.50         2.66 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       13.55        13.22        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.43        13.38        12.59        13.25        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY 
       12.76        12.85        15.52        12.33        25.25        12.03 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 
       13.18         0.13        12.85         5.06         6.35         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU 
        2.30        12.69         3.42        25.81        12.43        18.31 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       28.11        18.18         9.17        15.91        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4279 TCGA-BR-6709 
       14.37         2.10         6.61         6.97         9.57        12.16 
TCGA-BR-7723 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8365 TCGA-BR-8486 
       28.73         9.60         2.66         7.40        17.52        20.22 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 
       34.98         1.48         0.72        13.51         1.15        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-A48A TCGA-CG-4437 TCGA-CG-4443 
       13.15        13.35         7.17        12.43         8.05        29.98 
TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6527 
       12.03        12.03        12.66        20.91        18.54        10.26 
TCGA-D7-6815 TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-7916 TCGA-FP-8211 TCGA-HJ-7597 
       15.98        19.96         0.62        14.07        13.58        26.47 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 
       28.96         0.76        22.75         2.10        23.84        21.17 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A805 
       13.35         6.44        14.04        45.67        18.21         9.24 
TCGA-RD-A8MW TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS 
       37.91        48.79        13.25        37.41        17.85        13.35 
TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
       20.81        55.56         9.04        21.04        42.54        11.24 
TCGA-VQ-AA6K 
       12.43 

$`11Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU 
       24.00        19.99        22.82         0.36        35.97         5.16 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        9.86        26.93        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
        7.63        13.94         8.94        16.24        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS 
       33.27        35.21         0.85        20.78         2.63         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP 
        9.30         0.53        17.03         0.79        12.82        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON 
        6.28        30.25        26.33        32.61        21.01        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       25.12         7.40         3.75        12.92        13.48        16.47 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       52.57        46.09         5.92        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 
       15.35        12.62        12.46        12.59        22.39        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       12.33        13.22         4.47        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18        12.33        13.38        12.03        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30        15.78         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27         8.98        27.09        22.82 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        1.55         8.12        33.70        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24        18.21         3.42         1.32         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        9.44         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       37.25        14.43        11.44         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42        19.96         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        6.18        31.10        13.08         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        7.53         6.08        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42        21.44        16.14         5.13        13.41 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        19.07         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        15.22        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       20.32        22.29        15.65         8.38         4.34         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       19.53        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        0.10         6.51         6.58        20.25         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       29.00        23.80        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        3.72        19.73         8.52        74.53         6.08         4.60 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       16.87        19.04         5.79         0.92         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        43.36        21.73        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        18.74        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       60.85         9.50         9.73         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 
        6.58         5.72        66.81         2.66        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.13               0.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             55.56             122.30 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             12.85              14.94 
[1] "0.1 - 55.6 (12.8)"  "0.0 - 122.3 (14.9)"
[1] "hr=" "1.3"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         2        6        3        9        17        14
  11Q LOSS WILD-TYPE       8       15       44       24        70        73
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED          11         17          9         13        8
  11Q LOSS WILD-TYPE        17         78         63         33       41
                    vv
clus                 STAGE IVA
  11Q LOSS MUTATED           2
  11Q LOSS WILD-TYPE         2
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  6                 15
  STAGE IB                  3                 44
  STAGE II                  9                 24
  STAGE IIA                17                 70
  STAGE IIB                14                 73
  STAGE III                11                 17
  STAGE IIIA               17                 78
  STAGE IIIB                9                 63
  STAGE IIIC               13                 33
  STAGE IV                  8                 41
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11Q LOSS MUTATED      13  30  53  18
  11Q LOSS WILD-TYPE    42 106 230 106
D63V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               13                 42
  T2                  30                106
  T3                  53                230
  T4                  18                106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q LOSS MUTATED    34  42  14  22
  11Q LOSS WILD-TYPE 173 145  84  74
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               34                173
  N1               42                145
  N2               14                 84
  N3               22                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    93   8
  11Q LOSS WILD-TYPE 431  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     93    8
  11Q LOSS WILD-TYPE  431   31
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               93                431
  1                8                 31
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    25  97
  11Q LOSS WILD-TYPE 160 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     25   97
  11Q LOSS WILD-TYPE  160  343
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               25                160
  MALE                 97                343
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    81  31
  11Q LOSS WILD-TYPE 364  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     81   31
  11Q LOSS WILD-TYPE  364   88
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                81                364
  YES               31                 88
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED      30                         5
  11Q LOSS WILD-TYPE   104                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           0    74
  11Q LOSS WILD-TYPE                                         1   318
D63V11, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                                   30                104
  BLACK OR AFRICAN AMERICAN                                5                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   74                318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     5  74
  11Q LOSS WILD-TYPE   6 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      5   74
  11Q LOSS WILD-TYPE    6  330
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  6
  NOT HISPANIC OR LATINO               74                330
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    49  46
  12P LOSS WILD-TYPE 305 199
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                95                504 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                46                199 
$`12P LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-S8-A6BV TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH 
       34.85         8.94        20.02        27.35        25.78        31.27 
TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A97H 
       13.94        32.45        33.27         3.88         0.79        14.50 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OQ 
       47.38        25.22        30.25        32.61         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
       58.59         7.13         3.75         3.02        55.50        12.92 
TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FQ TCGA-Q9-A6FW 
       52.57        12.66        12.00        12.03        12.85         7.82 
TCGA-R6-A6KZ TCGA-V5-A7RC TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-BR-4183 
        5.06         3.42        18.21         2.10        19.73         6.61 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 
        4.08         9.67         6.18        17.29        35.24        33.63 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8687 
        3.45        11.44         5.39         9.21         9.86         8.22 
TCGA-BR-A4J6 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8535 TCGA-CD-A486 
        0.66        13.15        13.35         7.17        12.82         6.31 
TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4477 
       11.31        12.20        20.02         7.99        29.98        30.97 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-5647 
       15.02        69.04        15.22        12.33        14.27         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4H2 
        7.99        72.23         0.56        18.15        11.77        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-KB-A93J TCGA-MX-A666 
       23.84        23.80        13.35        19.53        36.95        14.04 
TCGA-R5-A7O7 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PS 
       45.67         5.46        13.02        12.79         2.70        13.35 
TCGA-VQ-A8PY TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D 
       14.33         9.50        55.56         2.01         4.54        66.81 
TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       21.04        11.24        43.66        16.14         0.79 

$`12P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.15         9.86        26.93        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL 
        5.92         8.94        16.24         4.21         7.69        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.16         0.30        26.33        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.32         3.16         4.90        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ 
        2.60        25.12         7.40         2.66        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       10.52        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        12.03        12.26        33.11         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        3.42         1.32         2.66        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 
        7.43        18.35        30.90         4.08         9.34         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       44.94        21.90         9.21        36.16        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72        25.18        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        32.58        20.88        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
       21.44        16.14         5.13        13.41        13.02        13.18 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       11.21        12.10        12.76        12.59        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.43        12.30        12.43        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       12.62         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       54.08         4.01        14.01        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        12.00         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       17.19        18.21        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        4.34        19.96         7.13        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H6 
        6.58        20.25         0.26         2.10        29.00        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39        18.38        12.46         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE 
        5.56        63.62        37.64         3.72        19.73        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       60.85         9.73         9.04        55.43         6.58         5.72 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        2.66        42.54        18.41        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        54.12        26.04        27.55        12.43        17.26 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.56               0.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             72.23             122.30 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            12.950             14.335 
[1] "0.6 - 72.2 (12.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         3        4       10        5        15        12
  12P LOSS WILD-TYPE       7       17       37       28        72        75
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           2         17         10          7        6
  12P LOSS WILD-TYPE        26         78         62         39       43
                    vv
clus                 STAGE IVA
  12P LOSS MUTATED           0
  12P LOSS WILD-TYPE         4
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  4                 17
  STAGE IB                 10                 37
  STAGE II                  5                 28
  STAGE IIA                15                 72
  STAGE IIB                12                 75
  STAGE III                 2                 26
  STAGE IIIA               17                 78
  STAGE IIIB               10                 62
  STAGE IIIC                7                 39
  STAGE IV                  6                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12P LOSS MUTATED      11  25  47  11
  12P LOSS WILD-TYPE    44 111 236 113
D64V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1               11                 44
  T2                  25                111
  T3                  47                236
  T4                  11                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P LOSS MUTATED    34  27  18  13
  12P LOSS WILD-TYPE 173 160  80  83
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               34                173
  N1               27                160
  N2               18                 80
  N3               13                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    80   5
  12P LOSS WILD-TYPE 444  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     80    5
  12P LOSS WILD-TYPE  444   34
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               80                444
  1                5                 34
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    31  67
  12P LOSS WILD-TYPE 154 373
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     31   67
  12P LOSS WILD-TYPE  154  373
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               31                154
  MALE                 67                373
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    77  12
  12P LOSS WILD-TYPE 368 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     77   12
  12P LOSS WILD-TYPE  368  107
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                77                368
  YES               12                107
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED      18                         4
  12P LOSS WILD-TYPE   116                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           0    60
  12P LOSS WILD-TYPE                                         1   332
D64V11, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                                   18                116
  BLACK OR AFRICAN AMERICAN                                4                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   60                332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  53
  12P LOSS WILD-TYPE  10 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   53
  12P LOSS WILD-TYPE   10  351
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               53                351
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    43  40
  12Q LOSS WILD-TYPE 311 205
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                83                516 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                40                205 
$`12Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-S8-A6BV TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GM 
       34.85         8.94        20.02        27.35        31.27        13.94 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       32.45        33.27         3.88         0.79        23.41        14.50 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OS 
       47.38        25.22        30.25        32.61         7.17        58.59 
TCGA-L5-A4OW TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L7-A56G 
        7.13         3.02        55.50         2.66        12.92        10.85 
TCGA-LN-A7HW TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-V5-A7RC 
       12.00        12.85         7.82         5.06         2.89         3.42 
TCGA-V5-AASX TCGA-VR-A8ET TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-BR-4183 TCGA-BR-4257 
        8.98         1.55        18.21        14.37         6.61         9.67 
TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 
       17.29        35.24        33.63         3.45        11.44        29.42 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4J6 TCGA-CD-5802 
        5.39         9.21         9.86         8.22         0.66        13.35 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4443 
        6.31        11.31        12.20        20.02         7.99        29.98 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6528 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
       15.02        69.04        15.22        15.65         0.62         7.99 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-IN-A6RN TCGA-IN-A6RP 
       13.58         0.56        11.77        12.95        19.53         6.44 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PH 
       37.64        45.67        18.21         5.46        18.48        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O 
       17.85        13.35        55.56         4.54        66.81        21.04 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       11.24        43.66        16.14        12.43         0.79 

$`12Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.15         9.86        26.93        25.78        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
        7.63         5.92         8.94        16.24         4.21         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.16         0.30        26.33        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         1.38         3.16         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NI 
       15.48         2.60        25.12         7.40         3.75        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         8.02         7.59        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29        16.44        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
       11.24         9.17        15.91        25.08        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 
        2.10         1.32         2.66        19.73        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       11.70        19.56        11.01         9.47         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.84        39.78        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
       29.59         9.60        32.25         8.05         0.56         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
        7.36        25.05         3.72        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 
       26.73        24.79        31.96        32.58        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.02        13.15        13.18        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        12.43        11.61         6.58        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34        19.96         7.13        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       17.06        59.54         5.03         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       12.46        13.35         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       36.95         3.72        19.73        14.04         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.25        13.02        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       34.29        46.26        16.31        22.19         2.50         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.50         9.73         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        5.72         2.66        42.54        18.41        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 
       32.94        17.13        54.12        26.04        27.55        17.26 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.56               0.00 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             69.04             122.30 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             12.95              14.07 
[1] "0.6 - 69.0 (12.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         3        3        7        3        13        15
  12Q LOSS WILD-TYPE       7       18       40       30        74        72
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0         12          9          8        4
  12Q LOSS WILD-TYPE        28         83         63         38       45
                    vv
clus                 STAGE IVA
  12Q LOSS MUTATED           1
  12Q LOSS WILD-TYPE         3
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  3                 18
  STAGE IB                  7                 40
  STAGE II                  3                 30
  STAGE IIA                13                 74
  STAGE IIB                15                 72
  STAGE III                 0                 28
  STAGE IIIA               12                 83
  STAGE IIIB                9                 63
  STAGE IIIC                8                 38
  STAGE IV                  4                 45
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12Q LOSS MUTATED      14  14  42  10
  12Q LOSS WILD-TYPE    41 122 241 114
D65V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               14                 41
  T2                  14                122
  T3                  42                241
  T4                  10                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q LOSS MUTATED    31  20  15  13
  12Q LOSS WILD-TYPE 176 167  83  83
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               31                176
  N1               20                167
  N2               15                 83
  N3               13                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    69   4
  12Q LOSS WILD-TYPE 455  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     69    4
  12Q LOSS WILD-TYPE  455   35
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               69                455
  1                4                 35
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    28  59
  12Q LOSS WILD-TYPE 157 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     28   59
  12Q LOSS WILD-TYPE  157  381
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               28                157
  MALE                 59                381
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    63  14
  12Q LOSS WILD-TYPE 382 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     63   14
  12Q LOSS WILD-TYPE  382  105
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                63                382
  YES               14                105
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED      11                         5
  12Q LOSS WILD-TYPE   123                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0    58
  12Q LOSS WILD-TYPE                                         1   334
D65V11, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                                   11                123
  BLACK OR AFRICAN AMERICAN                                5                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   58                334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2  46
  12Q LOSS WILD-TYPE   9 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   46
  12Q LOSS WILD-TYPE    9  358
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               46                358
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    60  41
  13Q LOSS WILD-TYPE 294 204
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               101                498 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                41                204 
$`13Q LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OE TCGA-CG-4475 TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK 
       60.39        24.00        22.98        25.78        58.55         7.63 
TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        8.94        32.45         7.69        35.21         0.85        20.78 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-JY-A6FA 
        3.88         0.53        17.03        23.41         9.96        44.75 
TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR 
       68.02        25.22        26.33        21.01        47.93         3.16 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS 
       29.00        15.48         3.75        13.22         5.49        13.41 
TCGA-L5-A8NU TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       83.24        10.85        10.36         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 
       13.41        13.38        13.15        15.35        13.25        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 
       12.76        12.59        22.39        12.85        13.22        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       10.52        12.23        12.03        12.33        13.38         0.13 
TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-VR-A8EO TCGA-VR-A8EP 
       12.26         5.06         6.35        12.69        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I 
       22.82        18.31        28.11        18.18        52.27        15.91 
TCGA-XP-A8T8 TCGA-3M-AB46 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-6456 
       14.37        58.03         6.61         6.97         4.08        17.29 
TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7716 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8486 
       26.10        12.16        39.78         7.40        31.10        20.22 
TCGA-BR-8683 TCGA-BR-A4IY TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8533 TCGA-CG-4301 
        9.86        12.89        12.59        12.53        15.39         3.02 
TCGA-CG-4466 TCGA-D7-6525 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-FP-7916 
       18.97        13.35        18.21        21.14        16.44        14.07 
TCGA-FP-8211 TCGA-HF-7133 TCGA-HU-A4GC TCGA-HU-A4H2 TCGA-IN-A6RJ TCGA-IN-A6RR 
       13.58        63.06         3.25        12.95        12.46         6.74 
TCGA-RD-A7BS TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91Z TCGA-VQ-A925 
       11.05         7.73         1.87        55.56         4.54 

$`13Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        21.99        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        27.35        26.93        31.27        14.30 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3YB 
        5.92        13.94        16.24         4.21        33.27         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP 
       20.12        18.64         9.30         0.79        12.82        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        14.50        12.16       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO 
        3.16        30.25         0.30        32.61        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        58.59         4.90         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49V 
        8.71        52.57        46.09        12.66        12.33        12.59 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.62        12.46        12.59        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FP 
        4.47        25.25        12.00        13.18        13.18        12.03 
TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.85        33.11         7.82         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       15.35         9.27         8.98        12.43         1.55         8.12 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       33.70        46.19        18.05        11.24         9.17        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        9.44         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 
       15.95        13.87        13.68        19.33        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        33.63        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        34.98         1.48        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 
       13.35        11.21        12.10        12.76         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        6.58        12.20        11.77        12.62        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        19.50        17.19        14.66        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       17.06        59.54         5.03         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.44        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO 
       22.19         2.50        12.79         2.70        17.85         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.13               0.00 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             83.24             122.30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            13.250             14.285 
[1] "0.1 - 83.2 (13.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         3        4        5        2        20        16
  13Q LOSS WILD-TYPE       7       17       42       31        67        71
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED          12         17          8          5        4
  13Q LOSS WILD-TYPE        16         78         64         41       45
                    vv
clus                 STAGE IVA
  13Q LOSS MUTATED           1
  13Q LOSS WILD-TYPE         3
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  4                 17
  STAGE IB                  5                 42
  STAGE II                  2                 31
  STAGE IIA                20                 67
  STAGE IIB                16                 71
  STAGE III                12                 16
  STAGE IIIA               17                 78
  STAGE IIIB                8                 64
  STAGE IIIC                5                 41
  STAGE IV                  4                 45
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  13Q LOSS MUTATED      13  23  52  11
  13Q LOSS WILD-TYPE    42 113 231 113
D66V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               13                 42
  T2                  23                113
  T3                  52                231
  T4                  11                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q LOSS MUTATED    40  39  10   9
  13Q LOSS WILD-TYPE 167 148  88  87
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               40                167
  N1               39                148
  N2               10                 88
  N3                9                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    85   3
  13Q LOSS WILD-TYPE 439  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     85    3
  13Q LOSS WILD-TYPE  439   36
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               85                439
  1                3                 36
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    20  83
  13Q LOSS WILD-TYPE 165 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     20   83
  13Q LOSS WILD-TYPE  165  357
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               20                165
  MALE                 83                357
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    69  28
  13Q LOSS WILD-TYPE 376  91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     69   28
  13Q LOSS WILD-TYPE  376   91
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                69                376
  YES               28                 91
[1] 2 2
[1] FALSE
D66V9, continuous
D66V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED      33                         2
  13Q LOSS WILD-TYPE   101                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           0    57
  13Q LOSS WILD-TYPE                                         1   335
D66V11, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                                   33                101
  BLACK OR AFRICAN AMERICAN                                2                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   57                335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     3  61
  13Q LOSS WILD-TYPE   8 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3   61
  13Q LOSS WILD-TYPE    8  343
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               61                343
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    87  66
  14Q LOSS WILD-TYPE 267 179
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               153                446 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                66                179 
$`14Q LOSS MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       60.39        18.28         8.94        24.00         4.70         0.36 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       27.35        26.93         7.63         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H 
       32.45        35.21        23.41        12.82         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
      122.10        47.38        25.22         0.30        26.33        32.61 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        3.16         7.13        15.48         3.75        55.50         2.66 
TCGA-L5-A8NJ TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49W TCGA-LN-A7HV 
       16.47        10.85        10.36        10.45        13.25        10.52 
TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       33.11         7.59         5.06         6.35         9.30        15.78 
TCGA-RE-A7BO TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-Z6-AAPN 
        7.00        25.81        22.82        52.27        18.05         2.66 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 
       19.56        11.01         9.44         6.61         4.08         9.67 
TCGA-BR-4279 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-6803 
        9.57        19.33        26.10         9.17        12.16        31.20 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8058 
       35.24        33.63        39.78        28.73        33.21        37.25 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 
       29.42         2.66        14.79         7.36         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 
        9.21        24.79        20.88         1.48         0.72         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-5803 
       32.52         0.46        20.65         1.15        13.18        11.21 
TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 
       12.76         7.17        15.39        12.07        12.82        11.31 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4477 
       12.20        20.02         7.99         8.05        54.08        30.97 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       20.55        18.84        18.54        17.19        10.26        15.98 
TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 
       14.66        16.44        11.31        22.29        19.96         7.99 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8245 
       11.38        14.07        17.06         0.56        26.47        18.15 
TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H4 
       28.96         3.25        11.77         8.98         2.10        23.84 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU 
       33.40        36.36        13.35         6.44         6.74        11.70 
TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A666 TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
        2.53        37.64        14.04        16.67        37.91       115.69 
TCGA-RD-A8N6 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 
        8.94         5.46        13.02        18.48        43.36         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PX TCGA-VQ-A8PY 
       46.26        12.79         2.70        17.85        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-AA6A 
       73.41        20.81        55.56        66.81        21.04        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       32.94        26.04         0.79 

$`14Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        34.85         4.31        19.99        22.82        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RE 
       31.27        14.30        58.55         5.92        13.94         7.69 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS 
        3.88         9.30         0.53        17.03         0.79         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       30.25        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88V 
        1.38        58.59         4.90        29.00         7.43         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
       25.12         7.40         3.02        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        46.09         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        25.25        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.85        12.26         7.82         8.02        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
       38.40        53.95         2.89         2.30        12.69        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        18.18        46.19        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK 
        1.32        19.73        58.03        26.70        11.70         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       17.29        13.68        39.12        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        40.21        30.90        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
        9.21        36.16        35.84        18.15        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        9.07        29.56        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
        9.60        32.25         8.05         0.56        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
        3.32        11.80        31.27        25.05         3.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        7.53        26.73        31.96        32.58         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       28.34        13.51        20.42        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8525 
       13.41        13.02        13.15        13.35        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        12.30        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        12.00         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
        7.99        25.71        12.66        20.91        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.85        13.35        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        26.43        11.24        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34         7.13         0.62        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         3.48        19.53        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       13.58         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       30.51         1.51         5.92        24.39        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20        22.75        25.81        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 
       23.80        21.17        14.07        15.68         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39        18.38        12.46        19.53        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       10.62        15.75        13.51         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
      122.30        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31        22.19         2.50         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       15.65        13.35        29.59        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        18.74        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58         5.72         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       43.66        28.41        17.13        54.12        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               0.3                0.0 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             122.1              122.3 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             14.66              13.63 
[1] "0.3 - 122.1 (14.7)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         4        3        9       11        21        20
  14Q LOSS WILD-TYPE       6       18       38       22        66        67
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           7         29         21         10        5
  14Q LOSS WILD-TYPE        21         66         51         36       44
                    vv
clus                 STAGE IVA
  14Q LOSS MUTATED           3
  14Q LOSS WILD-TYPE         1
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   4                  6
  STAGE IA                  3                 18
  STAGE IB                  9                 38
  STAGE II                 11                 22
  STAGE IIA                21                 66
  STAGE IIB                20                 67
  STAGE III                 7                 21
  STAGE IIIA               29                 66
  STAGE IIIB               21                 51
  STAGE IIIC               10                 36
  STAGE IV                  5                 44
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  14Q LOSS MUTATED      12  28  81  27
  14Q LOSS WILD-TYPE    43 108 202  97
D67V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1               12                 43
  T2                  28                108
  T3                  81                202
  T4                  27                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q LOSS MUTATED    47  45  32  20
  14Q LOSS WILD-TYPE 160 142  66  76
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               47                160
  N1               45                142
  N2               32                 66
  N3               20                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   129   6
  14Q LOSS WILD-TYPE 395  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    129    6
  14Q LOSS WILD-TYPE  395   33
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              129                395
  1                6                 33
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    45 112
  14Q LOSS WILD-TYPE 140 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     45  112
  14Q LOSS WILD-TYPE  140  328
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               45                140
  MALE                112                328
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   115  28
  14Q LOSS WILD-TYPE 330  91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    115   28
  14Q LOSS WILD-TYPE  330   91
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               115                330
  YES               28                 91
[1] 2 2
[1] FALSE
D67V9, continuous
D67V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED      30                         4
  14Q LOSS WILD-TYPE   104                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           0   106
  14Q LOSS WILD-TYPE                                         1   286
D67V11, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                                   30                104
  BLACK OR AFRICAN AMERICAN                                4                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  106                286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  98
  14Q LOSS WILD-TYPE  10 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   98
  14Q LOSS WILD-TYPE   10  306
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               98                306
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    89  54
  15Q LOSS WILD-TYPE 265 191
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               143                456 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                54                191 
$`15Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       34.85        18.28         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       27.12        20.02         0.23         9.86        27.35        26.93 
TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YC 
        5.92        16.24        32.45         7.69        35.21        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A93C TCGA-JY-A93D 
       18.64         3.88         4.67        14.50        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OT TCGA-L5-A4OU 
       25.22         0.30        32.61        47.93         4.90        29.00 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN 
        3.02        55.50         2.66        12.92        13.48         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MQ 
        8.71        13.41        83.24        12.59        22.39        12.33 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        25.25        12.03        13.38        12.03        12.85 
TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-RE-A7BO TCGA-V5-A7RE TCGA-VR-A8EO 
       12.26         5.06        38.40         7.00        16.44        25.81 
TCGA-VR-A8EU TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN 
       18.31        18.21        25.08        14.37         2.10         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-7704 TCGA-BR-7723 
       19.73        58.03        11.01         9.67        35.24        28.73 
TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8686 
        3.45        29.42         2.66        14.79         5.39        20.88 
TCGA-BR-8690 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8525 
       10.68         0.72        20.65        21.44        13.18        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A48C 
       12.53         7.17        12.39        12.82        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-5719 
       12.20        20.02         7.99         4.01        18.97         1.02 
TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 
       12.03        12.66        19.13        20.55        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 
       15.22        12.79        14.66        16.44        11.31        22.29 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-7998 TCGA-FP-A4BF TCGA-HJ-7597 
       15.65        19.96         7.99        22.29         5.52        26.47 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU 
       18.15        28.96        22.82        22.75         8.98         6.58 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RJ 
        2.10        12.95        23.84        21.17        33.40        12.46 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IP-7968 TCGA-R5-A7ZF TCGA-RD-A7BS 
       13.35         6.44        11.70         2.53         8.52        11.05 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT 
       16.67        37.91       115.69        35.61         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
        5.46        13.35        73.41         1.71         9.50         9.73 
TCGA-VQ-A922 TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F 
        9.04        42.54        43.66        32.94        54.12 

$`15Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        47.05        21.99        22.98        79.07        16.24 
TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.15        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       13.94         8.94         4.21        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82         9.96        14.86        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F 
       68.02         3.68        41.52        47.38        21.70        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON 
        6.28         3.16        30.25        26.33        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        3.32         7.17         1.38         3.16        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV 
       16.47        13.55        13.22         7.76        21.37        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59        12.85        15.52        11.54        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       10.52        12.00        12.23        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
        0.13        33.11         7.82         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        2.30        12.69        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD 
       18.05        11.24         9.17        15.91        41.23         3.42 
TCGA-Z6-A9VB TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
        1.32        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       39.78        18.15        15.32         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       32.25         8.05         0.56        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       11.80        31.27         7.36        25.05         3.72        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       32.58         9.86         8.22        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.76        12.33        12.30        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG 
       12.07        12.43         6.31        12.30        11.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
       36.00         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       25.71        20.91        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       13.35        15.98        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44        20.32         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        1.51         5.92        24.39        22.32        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
       20.25         0.26        29.00        23.80        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN 
       36.36         3.45        18.81         3.39        18.38        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        9.24         8.61         5.13       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87        19.04         0.92 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       14.33        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A923 
       20.81        32.88        42.64        60.85        55.56         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
        2.66        11.24        18.41        28.41        38.93        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.23               0.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            115.69             122.30 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            13.410             14.025 
[1] "0.2 - 115.7 (13.4)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         3        2       10        7        21        21
  15Q LOSS WILD-TYPE       7       19       37       26        66        66
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           8         30         18          9        9
  15Q LOSS WILD-TYPE        20         65         54         37       40
                    vv
clus                 STAGE IVA
  15Q LOSS MUTATED           2
  15Q LOSS WILD-TYPE         2
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  2                 19
  STAGE IB                 10                 37
  STAGE II                  7                 26
  STAGE IIA                21                 66
  STAGE IIB                21                 66
  STAGE III                 8                 20
  STAGE IIIA               30                 65
  STAGE IIIB               18                 54
  STAGE IIIC                9                 37
  STAGE IV                  9                 40
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  15Q LOSS MUTATED      14  31  82  18
  15Q LOSS WILD-TYPE    41 105 201 106
D68V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1               14                 41
  T2                  31                105
  T3                  82                201
  T4                  18                106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q LOSS MUTATED    46  51  24  21
  15Q LOSS WILD-TYPE 161 136  74  75
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               46                161
  N1               51                136
  N2               24                 74
  N3               21                 75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   123  10
  15Q LOSS WILD-TYPE 401  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    123   10
  15Q LOSS WILD-TYPE  401   29
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              123                401
  1               10                 29
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    42 107
  15Q LOSS WILD-TYPE 143 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     42  107
  15Q LOSS WILD-TYPE  143  333
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               42                143
  MALE                107                333
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   100  36
  15Q LOSS WILD-TYPE 345  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    100   36
  15Q LOSS WILD-TYPE  345   83
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               100                345
  YES               36                 83
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED      37                         3
  15Q LOSS WILD-TYPE    97                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           0    94
  15Q LOSS WILD-TYPE                                         1   298
D68V11, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                                   37                 97
  BLACK OR AFRICAN AMERICAN                                3                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   94                298
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     4  94
  15Q LOSS WILD-TYPE   7 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4   94
  15Q LOSS WILD-TYPE    7  310
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               94                310
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    88  60
  16P LOSS WILD-TYPE 266 185
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               148                451 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                60                185 
$`16P LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-Q9-A6FU 
       34.85        18.28        24.00         4.70         0.36         5.16 
TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       16.24        27.35        26.93         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3YC TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E 
        8.94        32.45        20.12        47.38        23.18        25.22 
TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.16        32.61        21.01         3.16        58.59         4.90 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NU 
        7.40         3.75         3.02        12.92         5.49        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49V 
       52.57        46.09        10.45        12.43        13.41        12.59 
TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A7HW TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6XQ 
       22.39        12.33        12.00        12.26         8.02         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
       53.95         9.30         2.30        12.69         7.00         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8Q7 
        3.42        16.44         9.27        27.09        22.82        52.27 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-7197 TCGA-BR-7704 
        2.10         2.66         6.61         4.08         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 
       33.63        39.78         3.45        33.21        11.44         0.69 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8677 
       29.42         2.66        19.96        17.52        14.79        26.73 
TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF 
       24.79         8.22        34.98         1.48         0.72         1.15 
TCGA-BR-A4QI TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 
       21.44        11.21        12.76        12.59        12.53        12.39 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4443 
        6.31        12.43        11.61        12.20         7.99        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6528 
       19.07        12.03        12.03        20.91        20.55        15.22 
TCGA-D7-6822 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A 
       12.33        11.31        22.29        15.65         8.38        19.96 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 
        7.99        72.23        63.06         5.92        18.15        22.82 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H4 
        0.76        22.75        25.81        11.77         6.58        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RN TCGA-IN-A6RR TCGA-KB-A6F5 
       23.80        21.17        33.40        19.53         6.74         5.56 
TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N9 
       37.64        14.04         6.08        11.05        16.67        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PE 
        5.79        48.79         5.46        18.48        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91A 
       12.79         2.70        17.85         1.87        64.57        39.45 
TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-AA68 
       18.74         9.50        55.56         9.04        66.81        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       38.93        17.13        27.55         0.79 

$`16P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         4.31         8.94        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       35.97        27.12        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GH 
       79.07         0.23        20.15         9.86        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 
       14.30        58.55        16.24         4.21         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
       44.75        68.02         3.68        41.52        21.70        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM 
       24.03         6.28        30.25         0.30        26.33        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         3.32         7.17         1.38        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NF 
        7.43        15.48         2.60        25.12        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
        8.71        13.41        10.85        10.36         5.92        12.66 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.76        12.59        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W5 
        7.59         5.06        16.31         7.04        38.40        15.78 
TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER 
        2.89        20.38        15.35         8.98        25.81        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       25.08        41.23        14.37         3.42         1.32        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       44.94        21.90        36.16        35.84        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
       28.73         9.07        29.56        37.25        14.43        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 
        9.60        32.25         8.05         0.56         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
       28.14         6.28         7.53        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       13.18        13.35        12.10         7.17        12.33        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.30        11.31         6.58        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
        4.01        14.01         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        12.36        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        4.34         7.13         0.62        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.32        21.07        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       24.20         3.25        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
       18.38        12.46        13.35         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
       10.62        11.70        15.75        13.51         2.53        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        19.73        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
       74.53         4.60         9.24         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        16.87        19.04         0.92        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       30.97        34.29        16.31         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        13.35        29.59        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       60.85         9.73         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       28.41        32.94        54.12        26.04        16.14        12.43 
TCGA-ZA-A8F6 
       17.26 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.36               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             83.24             122.30 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            13.165             14.040 
[1] "0.4 - 83.2 (13.2)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1"  
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         4        6       11        9        21        19
  16P LOSS WILD-TYPE       6       15       36       24        66        68
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           7         29         15          8        9
  16P LOSS WILD-TYPE        21         66         57         38       40
                    vv
clus                 STAGE IVA
  16P LOSS MUTATED           0
  16P LOSS WILD-TYPE         4
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   4                  6
  STAGE IA                  6                 15
  STAGE IB                 11                 36
  STAGE II                  9                 24
  STAGE IIA                21                 66
  STAGE IIB                19                 68
  STAGE III                 7                 21
  STAGE IIIA               29                 66
  STAGE IIIB               15                 57
  STAGE IIIC                8                 38
  STAGE IV                  9                 40
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16P LOSS MUTATED      17  28  74  24
  16P LOSS WILD-TYPE    38 108 209 100
D69V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1               17                 38
  T2                  28                108
  T3                  74                209
  T4                  24                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P LOSS MUTATED    48  54  21  18
  16P LOSS WILD-TYPE 159 133  77  78
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               48                159
  N1               54                133
  N2               21                 77
  N3               18                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   131   5
  16P LOSS WILD-TYPE 393  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    131    5
  16P LOSS WILD-TYPE  393   34
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0              131                393
  1                5                 34
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    45 109
  16P LOSS WILD-TYPE 140 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     45  109
  16P LOSS WILD-TYPE  140  331
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               45                140
  MALE                109                331
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   112  29
  16P LOSS WILD-TYPE 333  90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    112   29
  16P LOSS WILD-TYPE  333   90
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO               112                333
  YES               29                 90
[1] 2 2
[1] FALSE
D69V9, continuous
D69V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED      33                         5
  16P LOSS WILD-TYPE   101                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           0    95
  16P LOSS WILD-TYPE                                         1   297
D69V11, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                                   33                101
  BLACK OR AFRICAN AMERICAN                                5                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   95                297
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  89
  16P LOSS WILD-TYPE   8 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   89
  16P LOSS WILD-TYPE    8  315
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               89                315
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    98  64
  16Q LOSS WILD-TYPE 256 181
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               162                437 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                64                181 
$`16Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       34.85        18.28         8.94        24.00         4.70         0.36 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU 
        5.16        47.05        22.98        16.24        20.15        27.35 
TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       26.93        31.27         7.63         5.92         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A93C 
       32.45        35.21        20.12        14.50        47.38        23.18 
TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.16        32.61        21.01         3.16        58.59         4.90 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU 
        3.75         3.02        55.50         5.49         8.71        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V 
       46.09        10.85        10.36        10.45        13.41        12.59 
TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       12.33        10.52         5.06         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         2.30        12.69         7.00         5.29        16.44 
TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-XP-A8T6 TCGA-Z6-AAPN TCGA-3M-AB46 
        9.27        27.09        22.82        25.08         2.66        58.03 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-7197 
        9.44         6.61         4.08        17.29        26.10         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 
       35.24        33.63        39.78        28.73         3.45        33.21 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       11.44         0.69         9.60        29.42         2.66        19.96 
TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8687 
       17.52        14.79        25.18        26.73        24.79         8.22 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 
        0.72        20.65         1.15        21.44        13.15        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8534 
       11.21        12.76        12.59        12.53        12.39        12.07 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4449 
        6.31        12.43        12.20         7.99        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4477 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 
       12.03        30.97        12.03        20.91        20.55        17.19 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A6EX TCGA-D7-A6F0 
       15.22        12.79        18.21        14.27        11.31        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-F1-6875 TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8245 
       15.65         8.38        72.23        63.06         5.92        18.15 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H4 
       22.82         0.76        11.77         6.58         0.26        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-KB-A6F5 
       23.80        21.17        33.40        18.38        19.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A8N9 TCGA-SW-A7EB 
       63.62        37.64         6.08        11.05        35.61         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       48.79         5.46        18.48         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91A 
       12.79         2.70        17.85         1.87        64.57        39.45 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       18.74        32.88         9.50         9.73        55.56         9.04 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-ZQ-A9CR 
        4.54        66.81        43.66        38.93        17.13         0.79 

$`16Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        60.39         4.31        19.99        22.82        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 
       27.12        20.02        21.99        79.07         0.23         9.86 
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       25.78        14.30        58.55        13.94         4.21         7.69 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       68.02         3.68        41.52        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM 
       24.03         6.28        30.25         0.30        26.33        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         3.32         7.17         1.38        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NF 
        7.43        15.48         2.60        25.12         7.40         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       21.37        13.41        52.57         5.92        12.66        12.43 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        15.52        11.54        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX 
       38.40        15.78        20.38         3.42        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       25.81        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        18.21        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.01         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 
       21.90        36.16        35.84        18.15        15.32         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       29.56        37.25        14.43        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.56         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        22.19         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 
       27.12         9.34        28.14         6.28         7.53        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86        20.88        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52        13.51         0.46        20.42        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8527 TCGA-CD-8528 
       13.41        13.02        13.18        12.10         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
       12.30        12.59        11.64        15.39        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31        11.61         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       54.08         4.01        14.01         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        12.00         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       10.26        15.98        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.24        11.44        20.32         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51        26.47         1.51        24.39        28.96        22.32 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51        20.25         2.10        12.95        29.00 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93J 
       10.62        11.70        15.75        13.51         2.53        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       74.53         4.60         9.24         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV 
       57.44         8.94        16.87        19.04         0.92        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       30.97        34.29        16.31         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        13.35        29.59        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        20.81         1.71        42.64        60.85 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       42.54        11.24        18.41        28.41        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.26               0.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             83.24             122.30 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            14.645             13.870 
[1] "0.3 - 83.2 (14.6)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         5        6       13       12        19        20
  16Q LOSS WILD-TYPE       5       15       34       21        68        67
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           8         32         16         10        8
  16Q LOSS WILD-TYPE        20         63         56         36       41
                    vv
clus                 STAGE IVA
  16Q LOSS MUTATED           1
  16Q LOSS WILD-TYPE         3
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   5                  5
  STAGE IA                  6                 15
  STAGE IB                 13                 34
  STAGE II                 12                 21
  STAGE IIA                19                 68
  STAGE IIB                20                 67
  STAGE III                 8                 20
  STAGE IIIA               32                 63
  STAGE IIIB               16                 56
  STAGE IIIC               10                 36
  STAGE IV                  8                 41
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16Q LOSS MUTATED      17  31  80  28
  16Q LOSS WILD-TYPE    38 105 203  96
D70V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               17                 38
  T2                  31                105
  T3                  80                203
  T4                  28                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16Q LOSS MUTATED    52  52  25  23
  16Q LOSS WILD-TYPE 155 135  73  73
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               52                155
  N1               52                135
  N2               25                 73
  N3               23                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   142   5
  16Q LOSS WILD-TYPE 382  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    142    5
  16Q LOSS WILD-TYPE  382   34
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              142                382
  1                5                 34
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    52 115
  16Q LOSS WILD-TYPE 133 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     52  115
  16Q LOSS WILD-TYPE  133  325
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               52                133
  MALE                115                325
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   119  37
  16Q LOSS WILD-TYPE 326  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    119   37
  16Q LOSS WILD-TYPE  326   82
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               119                326
  YES               37                 82
[1] 2 2
[1] FALSE
D70V9, continuous
D70V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED      32                         6
  16Q LOSS WILD-TYPE   102                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           0   101
  16Q LOSS WILD-TYPE                                         1   291
D70V11, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                                   32                102
  BLACK OR AFRICAN AMERICAN                                6                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  101                291
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5  93
  16Q LOSS WILD-TYPE   6 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   93
  16Q LOSS WILD-TYPE    6  311
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  6
  NOT HISPANIC OR LATINO               93                311
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   138  94
  17P LOSS WILD-TYPE 216 151
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               232                367 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                94                151 
$`17P LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
       34.85        24.00         4.70         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A8PU 
       20.02        47.05        79.07         0.23         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ 
       26.93        25.78         7.63         5.92         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       32.45        18.64         3.88         0.79        23.41        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH 
      122.10        47.38        31.56        30.25        26.33        32.61 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        3.32         7.17         4.90         7.13         7.43         2.60 
TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
        3.75        16.47        13.22         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A1 
       83.24         5.92        10.45        13.15        13.25        12.59 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FQ TCGA-M9-A5M8 
       12.33        10.52        13.18        12.33        12.85        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.82         7.59         7.04        38.40         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        2.30        12.69         7.00        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EZ 
        8.98        27.09        22.82        12.43         8.12        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       52.27        11.24        18.21        25.08        14.37         2.66 
TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 
       58.03        11.70        11.01         9.44         6.61         9.67 
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 
        6.18        17.29        19.33         9.17        12.16         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8080 
       35.24        33.63        28.73        33.21         0.69         9.60 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8369 
       29.42         2.66        19.96        15.58        13.08        14.04 
TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
       14.79         5.39        25.18        24.79        32.58         9.86 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       10.68        13.87         7.53        34.98         1.48         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 
       13.51        20.65        20.42         1.15        13.02        13.15 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 
       12.76        12.59         7.17        12.33        12.30        15.39 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
       12.82         6.31        11.31        11.61        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         7.99         8.05        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5725 
       29.98        19.07         7.07        30.97         1.02        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        4.01        69.04        20.91        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
       13.35        17.19        10.26        15.22        15.98        11.31 
TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 
       14.66        16.44        11.31        15.65        19.96         7.99 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A9TM 
       72.23        11.38        14.07        17.06        13.58         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       77.29        63.06         1.51        18.15        28.96        22.82 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.75        11.77         8.98         6.58         2.10        12.95 
TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       23.80        36.36        18.81         3.39        18.38        13.35 
TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H 
       12.59        11.70        15.75         2.53         5.56        37.64 
TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 
       36.95        45.67         9.24         8.61        16.67       115.69 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       18.48        43.36         7.73        46.26        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       17.85         1.87        13.35        64.57        14.33        73.41 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A92D TCGA-VQ-A94T 
       18.74        20.81        42.64         9.50        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       16.14        27.55        12.43         0.79 

$`17P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        18.28         4.31         8.94        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-KB-A93G 
       22.82        35.97        21.99        22.98        16.24        20.15 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE 
       31.27        14.30        58.55        13.94        16.24         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        25.22        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.30        21.01        47.93        18.35         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
       58.59        29.00        15.48        25.12         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM 
       55.50         2.66        12.92        13.48        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49M 
       21.37        52.57        46.09        10.85        10.36        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.38        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A8I1 
       25.25        12.00        12.23        12.03        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.13        12.03        12.26         8.02         5.06        16.31 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        6.35        53.95         2.89        20.38         5.29         3.42 
TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D 
       25.81         1.55        18.31        28.11        33.70        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.05         9.17        15.91        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 
        1.32        19.73        26.70        19.56         9.47         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       21.90        36.16        35.84        39.78        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8297 
       29.59        32.25         8.05         0.56         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
       26.33         4.31         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       25.05         3.72         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       31.96        20.88         8.22        34.13         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        32.52         0.46        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8526 
       13.41        13.18        13.35        11.21        12.10        12.53 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A487 
       12.39        12.59        11.64        12.07        12.43        12.30 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 
       12.43         6.58        11.77        12.62        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 
       14.01        12.03         0.00         9.01        18.97        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       12.03        28.96        65.10        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-6818 
       12.66        19.13        18.61        17.85        12.79        12.36 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 
        8.38         4.34         7.13         0.62        14.47        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.48        19.53        22.29        59.54         5.03         0.56 
TCGA-FP-A4BF TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        5.52        52.21        30.51        26.47         5.92        24.39 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68        24.20         3.25        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10         6.51        20.25         0.26        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RJ 
       21.17        14.07        15.68        33.40         3.45        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X 
       19.53         6.44         6.74         6.51        10.62        13.51 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       63.62         3.72        19.73        14.04        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
       74.53         6.08         4.60        11.05         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       37.91        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       16.87        19.04        48.79        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       37.22        30.97        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D 
        9.27        23.41        15.65        29.59        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       21.83        61.22        32.88         1.71        60.85         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A 
        5.72        21.04         2.66        42.54        28.41        38.93 
TCGA-ZA-A8F6 
       17.26 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.23               0.00 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             122.1              122.3 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             13.30              14.43 
[1] "0.2 - 122.1 (13.3)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         5        8       18       15        26        35
  17P LOSS WILD-TYPE       5       13       29       18        61        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED          13         33         33         13       19
  17P LOSS WILD-TYPE        15         62         39         33       30
                    vv
clus                 STAGE IVA
  17P LOSS MUTATED           1
  17P LOSS WILD-TYPE         3
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   5                  5
  STAGE IA                  8                 13
  STAGE IB                 18                 29
  STAGE II                 15                 18
  STAGE IIA                26                 61
  STAGE IIB                35                 52
  STAGE III                13                 15
  STAGE IIIA               33                 62
  STAGE IIIB               33                 39
  STAGE IIIC               13                 33
  STAGE IV                 19                 30
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17P LOSS MUTATED      19  52 117  39
  17P LOSS WILD-TYPE    36  84 166  85
D71V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               19                 36
  T2                  52                 84
  T3                 117                166
  T4                  39                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P LOSS MUTATED    76  71  41  36
  17P LOSS WILD-TYPE 131 116  57  60
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               76                131
  N1               71                116
  N2               41                 57
  N3               36                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   200  12
  17P LOSS WILD-TYPE 324  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    200   12
  17P LOSS WILD-TYPE  324   27
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              200                324
  1               12                 27
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    59 178
  17P LOSS WILD-TYPE 126 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     59  178
  17P LOSS WILD-TYPE  126  262
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               59                126
  MALE                178                262
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   160  51
  17P LOSS WILD-TYPE 285  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    160   51
  17P LOSS WILD-TYPE  285   68
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               160                285
  YES               51                 68
[1] 2 2
[1] FALSE
D71V9, continuous
D71V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED      45                         7
  17P LOSS WILD-TYPE    89                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           1   145
  17P LOSS WILD-TYPE                                         0   247
D71V11, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                                   45                 89
  BLACK OR AFRICAN AMERICAN                                7                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  145                247
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     6 135
  17P LOSS WILD-TYPE   5 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6  135
  17P LOSS WILD-TYPE    5  269
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  5
  NOT HISPANIC OR LATINO              135                269
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    57  42
  17Q LOSS WILD-TYPE 297 203
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                99                500 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                42                203 
$`17Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A88Y TCGA-CG-4444 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U 
       34.85         0.36        47.05         0.23         9.86        26.93 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-L5-A4OW 
        8.94         4.21         0.79        23.41        14.50         7.13 
TCGA-L5-A891 TCGA-L5-A8NL TCGA-LN-A49L TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-LN-A9FQ 
        3.75        13.22        10.45        12.59        12.33        12.85 
TCGA-R6-A6Y2 TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.30        12.69        16.44         8.98        22.82        12.43 
TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-AAPN TCGA-B7-A5TJ 
       28.11        52.27        18.21        25.08         2.66        11.01 
TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7723 
        6.61         9.67        19.33         9.17        35.24        28.73 
TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8373 TCGA-BR-8485 
       33.21         0.69        19.96        15.58        14.79         9.21 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 
        9.86        10.68         7.53        34.98         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8533 
       20.65         1.15        13.02        12.76        12.33        15.39 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       12.82        11.31        11.61        12.20        20.02         3.02 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4477 TCGA-D7-5579 TCGA-D7-6519 
       54.08         4.01        19.07        30.97        20.91        20.55 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8576 TCGA-D7-A4YU 
       17.19        10.26        15.22        11.31        14.66        16.44 
TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GP 
       11.31        15.65         7.99        18.15        28.96         8.98 
TCGA-IN-8663 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A7C1 
        3.39         5.56        37.64        45.67         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PH 
      115.69         8.94         5.79         5.46        46.26        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y 
       17.85         1.87        64.57        18.74         9.50         9.73 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       32.94        27.55         0.79 

$`17Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       20.02        21.99        22.98        79.07        16.24        20.15 
TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       27.35        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        5.92        13.94        16.24        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30         0.53        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        7.43        15.48         2.60        25.12         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       52.57        46.09        10.85        10.36         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET 
        3.42        15.35         9.27        25.81        27.09         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31         8.12        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       11.24         9.17        15.91        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       19.56         9.47         9.44         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 
        8.05         0.56        29.42         2.66         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS 
       20.88         8.22        34.13        13.87         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
       28.34         0.66        32.52         0.46        20.42        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       16.14         5.13        13.41        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       11.21        12.10        12.59        12.53         7.17        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 
       12.39        12.59        11.64        12.07        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
       12.30        12.43         6.58        11.77        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         7.99         8.05        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       69.04        21.07         7.99        25.71        12.66        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       18.84        18.54        18.61        17.85        13.35        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19        18.21        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        22.29         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        14.04        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         9.24        11.05         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       19.04         0.92        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       30.97        34.29        16.31        22.19         2.50         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY 
        9.27        23.41        15.65        13.35        29.59        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       73.41        39.45        11.70        21.83        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 
       32.88         1.71        42.64        60.85        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.23               0.00 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            115.69             122.30 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             12.79              14.12 
[1] "0.2 - 115.7 (12.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0        1        7        6        10        16
  17Q LOSS WILD-TYPE      10       20       40       27        77        71
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           5         19         15          5        7
  17Q LOSS WILD-TYPE        23         76         57         41       42
                    vv
clus                 STAGE IVA
  17Q LOSS MUTATED           1
  17Q LOSS WILD-TYPE         3
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 20
  STAGE IB                  7                 40
  STAGE II                  6                 27
  STAGE IIA                10                 77
  STAGE IIB                16                 71
  STAGE III                 5                 23
  STAGE IIIA               19                 76
  STAGE IIIB               15                 57
  STAGE IIIC                5                 41
  STAGE IV                  7                 42
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17Q LOSS MUTATED       5  19  49  24
  17Q LOSS WILD-TYPE    50 117 234 100
D72V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                5                 50
  T2                  19                117
  T3                  49                234
  T4                  24                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q LOSS MUTATED    26  35  19  15
  17Q LOSS WILD-TYPE 181 152  79  81
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               26                181
  N1               35                152
  N2               19                 79
  N3               15                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    89   4
  17Q LOSS WILD-TYPE 435  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     89    4
  17Q LOSS WILD-TYPE  435   35
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               89                435
  1                4                 35
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    32  70
  17Q LOSS WILD-TYPE 153 370
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     32   70
  17Q LOSS WILD-TYPE  153  370
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               32                153
  MALE                 70                370
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    71  17
  17Q LOSS WILD-TYPE 374 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     71   17
  17Q LOSS WILD-TYPE  374  102
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                71                374
  YES               17                102
[1] 2 2
[1] FALSE
D72V9, continuous
D72V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED      20                         2
  17Q LOSS WILD-TYPE   114                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           1    63
  17Q LOSS WILD-TYPE                                         0   329
D72V11, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                                   20                114
  BLACK OR AFRICAN AMERICAN                                2                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   63                329
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4  65
  17Q LOSS WILD-TYPE   7 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4   65
  17Q LOSS WILD-TYPE    7  339
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               65                339
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   114  68
  18P LOSS WILD-TYPE 240 177
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               182                417 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                68                177 
$`18P LOSS MUTATED`
TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
       18.28        24.00         4.70        35.97         5.16        20.02 
TCGA-CG-4444 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI 
       47.05         0.23        20.15        26.93        25.78        14.30 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 
        5.92         8.94        16.24        32.45        33.27         0.85 
TCGA-IG-A3YB TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A93C 
        2.63         0.79        23.41        14.50        47.38        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A891 
       26.33        32.61         7.17         7.43        15.48         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
        8.71        52.57        10.36         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A4A1 TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FQ 
       13.41        12.33        12.59        12.03        13.18        12.85 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.82         7.59        38.40         6.35        53.95         9.30 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EW 
        2.30         7.00         9.27        27.09        18.31         8.12 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 
       18.21        41.23         3.42         2.66        19.73        58.03 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4255 TCGA-BR-4279 
       19.56        11.01         9.47         9.44         4.08         9.57 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 
       17.29        13.68        26.10        12.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8364 
       39.78        28.73         9.07         2.66        19.96        22.19 
TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8678 
        0.95        14.04        25.18        27.12        26.73        24.79 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86        20.88        10.68         7.53        34.98         1.48 
TCGA-BR-A4IY TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       12.89        13.18        11.21        12.76        12.59         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A489 
       12.33        12.30        11.64        15.39        12.07        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.43        11.61         7.99         8.05        54.08         4.01 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5732 TCGA-D7-6518 
       19.07         7.07        30.97         1.02        69.04        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-8573 TCGA-D7-8575 
       20.55        18.54        13.35        15.98        19.50        18.21 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-EQ-5647 
       21.14        16.44        36.43        11.24        20.32         0.62 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23        11.38        19.53        14.07        22.29        17.06 
TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G6 
        1.51        18.15        28.96        22.82        21.07        24.26 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 
       11.77         8.98         6.58         2.10        12.95        21.17 
TCGA-IN-A6RL TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J 
       13.35        11.70        13.51         5.56        37.64        36.95 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-SW-A7EB 
       45.67        18.21         8.52        16.67       115.69         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PD 
       48.79         5.46        13.02        18.48        43.36        16.31 
TCGA-VQ-A8PF TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R 
        2.50        42.64        55.56         4.54        66.81        42.54 
TCGA-VQ-AA6B TCGA-VQ-AA6K 
       32.94        12.43 

$`18P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        34.85         4.31         8.94        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       22.82         0.36        27.12        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       16.24         9.86        27.35        31.27        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
       13.94         4.21         7.69        35.21        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 
       18.64         3.88         9.30         0.53        17.03        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A4OJ 
       68.02         3.68        41.52        21.70         6.28        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.13         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS 
        3.02        13.48         7.76         5.49        21.37        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S 
       83.24        46.09        10.85        12.66        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       12.00        12.23        13.18        12.33        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.03        12.26        33.11         8.02         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
        7.04        15.78         2.89        12.69        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        3.42        16.44        15.35         8.98        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.43         1.55        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       46.19        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 
       14.37         2.10         1.32        26.70        11.70         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         6.18         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.87        19.33        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       44.94        21.90         9.21        36.16        35.84        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       15.32         3.45        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.56        29.42         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
       31.10        13.08         0.26        17.52        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 
        9.34        28.14         6.28         7.53        31.96        32.58 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        8.22        34.13        13.87         6.08        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 
       13.35        12.10        12.53        12.39        12.59        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.43         6.31        12.30         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        12.03         0.00         9.01        18.97 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       12.00         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       21.07         7.99        25.71        12.66        20.91        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       18.61        17.85        17.19        10.26        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       12.36        11.31        12.33        24.72        16.80        17.19 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.66        20.91        14.27         5.92        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.31        11.44        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 
        4.34        19.96         7.13         7.99        14.47        21.27 
TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
        3.48        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
        5.92        24.39        22.32         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
       29.98         0.10         6.51        20.25         0.26        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
        6.44         6.74        12.59         6.51        10.62        15.75 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI 
        2.53        63.62         3.72        19.73        14.04        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV 
        8.94        35.61        16.87        19.04         0.92        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.29        46.26        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       61.22        18.74        20.81        32.88         1.71        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.50         9.73         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        5.72        21.04         2.66        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        17.26         0.79 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.23               0.00 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            115.69             122.30 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             13.86              13.94 
[1] "0.2 - 115.7 (13.9)" "0.0 - 122.3 (13.9)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         3        5       11       11        27        22
  18P LOSS WILD-TYPE       7       16       36       22        60        65
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED          10         30         23         12       14
  18P LOSS WILD-TYPE        18         65         49         34       35
                    vv
clus                 STAGE IVA
  18P LOSS MUTATED           2
  18P LOSS WILD-TYPE         2
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  5                 16
  STAGE IB                 11                 36
  STAGE II                 11                 22
  STAGE IIA                27                 60
  STAGE IIB                22                 65
  STAGE III                10                 18
  STAGE IIIA               30                 65
  STAGE IIIB               23                 49
  STAGE IIIC               12                 34
  STAGE IV                 14                 35
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18P LOSS MUTATED      13  34  99  31
  18P LOSS WILD-TYPE    42 102 184  93
D73V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               13                 42
  T2                  34                102
  T3                  99                184
  T4                  31                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P LOSS MUTATED    60  52  32  29
  18P LOSS WILD-TYPE 147 135  66  67
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               60                147
  N1               52                135
  N2               32                 66
  N3               29                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   152  13
  18P LOSS WILD-TYPE 372  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    152   13
  18P LOSS WILD-TYPE  372   26
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              152                372
  1               13                 26
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    46 141
  18P LOSS WILD-TYPE 139 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     46  141
  18P LOSS WILD-TYPE  139  299
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               46                139
  MALE                141                299
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   139  31
  18P LOSS WILD-TYPE 306  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    139   31
  18P LOSS WILD-TYPE  306   88
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO               139                306
  YES               31                 88
[1] 2 2
[1] FALSE
D73V9, continuous
D73V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED      46                         4
  18P LOSS WILD-TYPE    88                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           0   116
  18P LOSS WILD-TYPE                                         1   276
D73V11, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                                   46                 88
  BLACK OR AFRICAN AMERICAN                                4                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  116                276
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     5 118
  18P LOSS WILD-TYPE   6 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5  118
  18P LOSS WILD-TYPE    6  286
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  6
  NOT HISPANIC OR LATINO              118                286
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   150 100
  18Q LOSS WILD-TYPE 204 145
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               250                349 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               100                145 
$`18Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       34.85        18.28         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX 
       27.12         5.16        20.02        47.05        22.98         0.23 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15        27.35        26.93        25.78        31.27        14.30 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB 
        8.94        16.24        32.45         7.69         0.85         2.63 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H 
        3.88         0.53         0.79        23.41         9.96        14.50 
TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       12.16        68.02        47.38        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO 
       24.03         3.16         0.30        26.33        32.61         3.32 
TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       16.47        13.55        13.22         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        10.85        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A5 
       13.41        12.33        13.38        13.25        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX 
       12.85        12.33        13.22         4.47        12.33        12.23 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.38        13.18        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.59        38.40         6.35        53.95         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU 
       12.69         7.00         9.27        27.09        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
        8.12        46.19        18.05         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 
       25.08        41.23         3.42         2.66        19.73        58.03 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 
        4.08         6.18         9.57        17.29        13.68        26.10 
TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7957 
       12.16        35.24        33.63        39.78        28.73         9.07 
TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 
       11.44        19.96        22.19         0.95        14.04         3.32 
TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 
       20.22        27.12        26.73        24.79         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4IY 
        8.22        10.68        13.87         7.53        34.98        12.89 
TCGA-BR-A4J6 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        0.66        13.18        13.35        11.21        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
       12.53         7.17        12.33        12.30        11.64        15.39 
TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 
       12.07         6.31        12.43        11.61        12.20         3.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4466 
        7.99         8.05        54.08         4.01        19.07        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 
        7.07        30.97         1.02        12.03         4.01        69.04 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       25.71        19.13        20.55        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       10.26        15.98        19.50        18.21        14.66        21.14 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       16.44        36.43        11.24        20.32        22.29        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 
       19.96         0.62         7.99        72.23        11.38        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       14.07        22.29        17.06        18.15        28.96        22.82 
TCGA-HU-8608 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 
       21.07        24.26        11.77         8.98         6.58         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
       12.95        21.17        13.35         6.74        10.62        11.70 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
       13.51         5.56        63.62        37.64        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-SW-A7EB TCGA-VQ-A8DT 
        8.52        16.67        37.91       115.69         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 
        5.46        13.25        13.02        18.48        43.36         7.73 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91V 
       16.31        22.19         2.50        17.85        13.35        42.64 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R 
        9.50        55.56         2.01         4.54        66.81        42.54 
TCGA-VQ-A94T TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6K 
       11.24        38.93        32.94        12.43 

$`18Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-2H-A9GJ TCGA-2H-A9GK 
       21.99        79.07        16.24         9.86        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        5.92        13.94         4.21        33.27        35.21        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP 
       20.12        18.64         9.30        17.03        12.82        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
        4.67       122.10        44.75         3.68        41.52        21.70 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
        6.28        30.25        21.01        47.93        18.35         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NM 
        3.16        58.59        25.12         7.40        13.48         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U 
        5.49        21.37        46.09         5.92        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.59        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
       15.52        11.54        25.25        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-R6-A6KZ 
       13.18        12.33         0.13        12.03        12.26         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RB 
       16.31         7.04         9.30        15.78        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        3.42        16.44        15.35         8.98        25.81        22.82 
TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
        1.55        28.11        33.70        18.18        52.27        11.24 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 
       14.37         2.10         1.32        26.70         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         9.34         9.67 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        19.33        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 
       36.16        35.84        18.15        15.32         3.45        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       32.25         8.05         0.56        29.42         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       17.52        26.33         4.31        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       31.96        32.58        34.13         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5804 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       12.10        12.39        12.59        12.82        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
       11.31         6.58        11.77        12.62        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 
       15.95         1.02        14.01        29.98        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
        9.01        12.00         6.97        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        15.02        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
        7.99        12.66        20.91        18.84        18.61        17.85 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY 
       16.80        17.19        20.91        14.27         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 
       14.76        26.43        11.31        11.44         8.38         4.34 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 
        7.13        14.47        21.27         3.48        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       22.32         0.76        24.30         5.59        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        22.75        25.81        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.51        20.25         0.26        29.00        23.84        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
        3.39        18.38        12.46        19.53         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        6.51        15.75         2.53        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       14.04        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       57.44         8.94        35.61        16.87        19.04         0.92 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
        1.71        60.85         9.73         9.04        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        5.72        21.04         2.66        18.41        43.66        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       17.13        54.12        26.04        16.14        27.55        17.26 
TCGA-ZQ-A9CR 
        0.79 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.23               0.00 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            115.69             122.30 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             13.35              14.79 
[1] "0.2 - 115.7 (13.3)" "0.0 - 122.3 (14.8)"
[1] "hr=" "1"  
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         3        6       18       13        38        36
  18Q LOSS WILD-TYPE       7       15       29       20        49        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED          14         41         32         15       18
  18Q LOSS WILD-TYPE        14         54         40         31       31
                    vv
clus                 STAGE IVA
  18Q LOSS MUTATED           2
  18Q LOSS WILD-TYPE         2
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  6                 15
  STAGE IB                 18                 29
  STAGE II                 13                 20
  STAGE IIA                38                 49
  STAGE IIB                36                 51
  STAGE III                14                 14
  STAGE IIIA               41                 54
  STAGE IIIB               32                 40
  STAGE IIIC               15                 31
  STAGE IV                 18                 31
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18Q LOSS MUTATED      18  56 136  34
  18Q LOSS WILD-TYPE    37  80 147  90
D74V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               18                 37
  T2                  56                 80
  T3                 136                147
  T4                  34                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q LOSS MUTATED    84  77  41  37
  18Q LOSS WILD-TYPE 123 110  57  59
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               84                123
  N1               77                110
  N2               41                 57
  N3               37                 59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   211  17
  18Q LOSS WILD-TYPE 313  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    211   17
  18Q LOSS WILD-TYPE  313   22
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              211                313
  1               17                 22
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    69 188
  18Q LOSS WILD-TYPE 116 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     69  188
  18Q LOSS WILD-TYPE  116  252
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               69                116
  MALE                188                252
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   181  52
  18Q LOSS WILD-TYPE 264  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    181   52
  18Q LOSS WILD-TYPE  264   67
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               181                264
  YES               52                 67
[1] 2 2
[1] FALSE
D74V9, continuous
D74V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED      59                         6
  18Q LOSS WILD-TYPE    75                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           0   158
  18Q LOSS WILD-TYPE                                         1   234
D74V11, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                                   59                 75
  BLACK OR AFRICAN AMERICAN                                6                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  158                234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     6 153
  18Q LOSS WILD-TYPE   5 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      6  153
  18Q LOSS WILD-TYPE    5  251
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  5
  NOT HISPANIC OR LATINO              153                251
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    97  80
  19P LOSS WILD-TYPE 257 165
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               177                422 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                80                165 
$`19P LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43J TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       34.85         4.31        27.35        25.78        31.27        14.30 
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A4QS 
        7.63        16.24         4.21         7.69         2.63         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6F8 
        0.53        17.03        23.41         9.96        14.50       122.10 
TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OP 
       68.02        47.38        30.25        26.33        47.93         7.17 
TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NJ 
       58.59         7.43         2.60         3.75         2.66        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW 
       13.55        13.22         5.49         8.71        52.57        46.09 
TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49Y 
       10.85        10.45        12.66        13.38        15.35        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX 
       12.59        12.49        12.85         4.47        12.33        12.23 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A8W5 
       13.18        13.38         8.02         5.06         7.04        15.78 
TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 
        3.42         9.27        25.81         8.12        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       46.19         9.17        25.08        14.37         2.66        19.73 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6565 
       19.56        11.01         9.44         6.61         9.67         9.17 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 
       35.24        33.63        39.78        28.73         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8485 
        0.69         2.66         2.20        14.04        14.79         9.21 
TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PD 
       24.79        10.68        34.98         1.48         0.72        20.65 
TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
        1.15        13.02        13.15        12.10        12.76        12.59 
TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 
        7.17         6.31        11.31        12.43        12.20        20.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4466 TCGA-CG-5724 
        7.99        54.08         4.01        29.98        18.97        12.03 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       15.02        69.04        18.84        13.35        17.19        10.26 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       12.79        11.31        19.50        11.31        22.29        15.65 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A9TM 
        0.62         7.99        72.23        17.06         0.56         6.21 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 
        5.92        18.15        11.77         8.98         6.58         2.10 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RS 
       23.84        23.80        33.40         3.39        18.38        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 
       10.62        11.70         5.56        63.62        37.64        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N6 
       18.21         6.08         8.61         5.13        37.91         8.94 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91N TCGA-VQ-A91U 
       43.36         7.73        17.85         1.87        18.74         1.71 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       42.64         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       21.04        43.66        38.93        17.13        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       27.55        12.43         0.79 

$`19P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GJ TCGA-2H-A9GL 
        0.23        20.15         9.86        26.93        58.55         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       13.94         8.94        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 
       20.78        20.12        18.64         9.30         0.79        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86         4.67        12.16        44.75         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        3.16         0.30        32.61        21.01        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        1.38         3.16         4.90        29.00         7.13        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         7.40         3.02        55.50        12.92        13.48 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K 
        7.76        21.37        13.41        83.24        10.36         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41        12.33        13.15        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.62        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
       12.33        13.22        25.25        10.52        12.00        12.03 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         7.82         7.59        16.31        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP 
       20.38         5.29        16.44        15.35         8.98        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31        28.11        33.70 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD 
       18.05        11.24        15.91        18.21        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK 
        2.10         1.32        58.03        26.70        11.70         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 
        9.21        36.16        35.84        18.15        15.32         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
       29.56        33.21        37.25        14.43        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 
       32.25         8.05         0.56        29.42        19.96        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88         8.22        34.13        13.87         7.53         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51         0.46        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
       21.44        16.14         5.13        13.41        13.18        13.35 
TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       11.21        12.53        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       11.64        15.39        12.07        12.82        12.43        12.30 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.61         6.58        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 
       15.95         1.02         8.05        14.01        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
       12.66        20.91        19.13        20.55        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       17.85        15.22        15.98        12.36        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        11.44        20.32         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       19.96         7.13        14.47        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        22.75        25.81        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H6 
        6.51        20.25         0.26        12.95        29.00        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ 
       14.07        15.68        36.36         3.45        18.81        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V 
       13.35        19.53         6.44         6.74         6.51        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       13.51         2.53        36.95         3.72        19.73        14.04 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 
        8.52        74.53         4.60         9.24        11.05        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       35.61        16.87        19.04         5.79        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19         2.50        12.79         2.70         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        20.81        32.88 
TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       60.85        55.43         4.54         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        42.54        11.24        18.41        28.41        32.94 
TCGA-VQ-AA6F TCGA-ZA-A8F6 
       54.12        17.26 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.53               0.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             122.1              122.3 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             12.66              15.27 
[1] "0.5 - 122.1 (12.7)" "0.0 - 122.3 (15.3)"
[1] "hr=" "1.3"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         3        7       11        7        28        30
  19P LOSS WILD-TYPE       7       14       36       26        59        57
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED          11         27         16         15       13
  19P LOSS WILD-TYPE        17         68         56         31       36
                    vv
clus                 STAGE IVA
  19P LOSS MUTATED           3
  19P LOSS WILD-TYPE         1
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  7                 14
  STAGE IB                 11                 36
  STAGE II                  7                 26
  STAGE IIA                28                 59
  STAGE IIB                30                 57
  STAGE III                11                 17
  STAGE IIIA               27                 68
  STAGE IIIB               16                 56
  STAGE IIIC               15                 31
  STAGE IV                 13                 36
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19P LOSS MUTATED      18  36  88  32
  19P LOSS WILD-TYPE    37 100 195  92
D75V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               18                 37
  T2                  36                100
  T3                  88                195
  T4                  32                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P LOSS MUTATED    56  58  24  32
  19P LOSS WILD-TYPE 151 129  74  64
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               56                151
  N1               58                129
  N2               24                 74
  N3               32                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   156  10
  19P LOSS WILD-TYPE 368  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    156   10
  19P LOSS WILD-TYPE  368   29
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              156                368
  1               10                 29
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    47 135
  19P LOSS WILD-TYPE 138 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     47  135
  19P LOSS WILD-TYPE  138  305
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               47                138
  MALE                135                305
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   127  37
  19P LOSS WILD-TYPE 318  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    127   37
  19P LOSS WILD-TYPE  318   82
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO               127                318
  YES               37                 82
[1] 2 2
[1] FALSE
D75V9, continuous
D75V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED      41                        10
  19P LOSS WILD-TYPE    93                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           1   104
  19P LOSS WILD-TYPE                                         0   288
D75V11, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                                   41                 93
  BLACK OR AFRICAN AMERICAN                               10                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  104                288
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3 105
  19P LOSS WILD-TYPE   8 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3  105
  19P LOSS WILD-TYPE    8  299
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO              105                299
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    83  55
  19Q LOSS WILD-TYPE 271 190
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               138                461 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                55                190 
$`19Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43J TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       34.85         4.31        27.35        25.78        31.27        14.30 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A6QS 
        4.21         7.69         2.63         0.53        23.41         9.96 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A4OM 
       14.50       122.10        68.02        47.38        30.25        47.93 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
        7.17        58.59         7.43        15.48         2.60         3.75 
TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
        2.66        13.22         8.71        10.85        10.45        12.66 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A5U5 
       13.38        13.15        12.46        12.59        12.49         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-R6-A6DN TCGA-R6-A8W5 
       12.33        12.23        13.18        13.38         8.02        15.78 
TCGA-R6-A8WC TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 
        2.30         3.42        25.81         8.12        18.18        52.27 
TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TJ 
        9.17        25.08        14.37         2.66        19.73        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7715 
        9.44         6.61         9.67         9.17        35.24        33.63 
TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 
       28.73        11.44         0.69         2.66         2.20        14.04 
TCGA-BR-8373 TCGA-BR-8678 TCGA-BR-A4CS TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 
       14.79        24.79         1.48        20.65         1.15        13.02 
TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A489 
       13.15        12.10        12.59         7.17         6.31        11.31 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4443 
       12.43        12.20        20.02         7.99         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6526 
       19.07        18.97        12.03        15.02        69.04        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A6EX 
       10.26        15.22        12.79        11.31        19.50        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 
       22.29        15.65         0.62        17.06         0.56         5.92 
TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H5 
       18.15        11.77         8.98         6.58        23.84        23.80 
TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 
       33.40        18.38        12.59        10.62        11.70         5.56 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BW TCGA-RD-A8MW TCGA-VQ-A8DT 
       37.64        45.67        18.21         5.13        37.91        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PK TCGA-VQ-A8PM 
        5.46        13.02        18.48        43.36        17.85         1.87 
TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O 
       18.74        42.64         9.50        55.56         9.04        21.04 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       38.93        17.13        26.04        16.14        27.55         0.79 

$`19Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GJ TCGA-2H-A9GK 
        0.23        20.15         9.86        26.93        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 
        5.92        13.94         8.94        16.24        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85        20.78        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
        9.30        17.03         0.79        12.82        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       12.16        44.75         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       26.33        32.61        21.01        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88W TCGA-L5-A88Z 
        3.16         4.90        29.00         7.13        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       46.09        10.36         5.92        12.43        13.41        12.33 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
       15.35        12.59        13.25        12.62        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 
       25.25        10.52        12.00        12.03        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       53.95         9.30         2.89        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        5.29        16.44        15.35         9.27         8.98        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31        28.11        33.70 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       46.19        18.05        11.24        15.91        18.21        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         1.32        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       44.94        21.90         9.21        36.16        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       37.25        14.43        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.56        29.42        19.96        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
       26.33         4.31         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42        21.44        16.14         5.13        13.41 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 
       13.18        13.35        11.21        12.76        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.82        12.43        12.30        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       12.62         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       54.08        14.01        12.03         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        28.96        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       15.98        12.36        12.33        24.72        16.80        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44        20.32         8.38         4.34        19.96         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       29.00        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
        6.74         6.51        15.75        13.51         2.53        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       36.95         3.72        19.73        14.04         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         8.61        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       12.79         2.70         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       21.83        61.22        20.81        32.88         1.71        60.85 
TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       66.81         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6K TCGA-ZA-A8F6 
       28.41        32.94        54.12        12.43        17.26 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.53               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             122.1              122.3 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             13.02              14.33 
[1] "0.5 - 122.1 (13.0)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         3        6       10        6        24        23
  19Q LOSS WILD-TYPE       7       15       37       27        63        64
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           7         19         14          9       11
  19Q LOSS WILD-TYPE        21         76         58         37       38
                    vv
clus                 STAGE IVA
  19Q LOSS MUTATED           2
  19Q LOSS WILD-TYPE         2
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   3                  7
  STAGE IA                  6                 15
  STAGE IB                 10                 37
  STAGE II                  6                 27
  STAGE IIA                24                 63
  STAGE IIB                23                 64
  STAGE III                 7                 21
  STAGE IIIA               19                 76
  STAGE IIIB               14                 58
  STAGE IIIC                9                 37
  STAGE IV                 11                 38
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19Q LOSS MUTATED      13  30  70  23
  19Q LOSS WILD-TYPE    42 106 213 101
D76V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1               13                 42
  T2                  30                106
  T3                  70                213
  T4                  23                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q LOSS MUTATED    50  41  18  24
  19Q LOSS WILD-TYPE 157 146  80  72
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               50                157
  N1               41                146
  N2               18                 80
  N3               24                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   120   9
  19Q LOSS WILD-TYPE 404  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    120    9
  19Q LOSS WILD-TYPE  404   30
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0              120                404
  1                9                 30
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    37 105
  19Q LOSS WILD-TYPE 148 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     37  105
  19Q LOSS WILD-TYPE  148  335
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               37                148
  MALE                105                335
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    98  28
  19Q LOSS WILD-TYPE 347  91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     98   28
  19Q LOSS WILD-TYPE  347   91
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                98                347
  YES               28                 91
[1] 2 2
[1] FALSE
D76V9, continuous
D76V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED      36                         8
  19Q LOSS WILD-TYPE    98                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           0    76
  19Q LOSS WILD-TYPE                                         1   316
D76V11, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                                   36                 98
  BLACK OR AFRICAN AMERICAN                                8                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   76                316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     3  83
  19Q LOSS WILD-TYPE   8 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3   83
  19Q LOSS WILD-TYPE    8  321
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               83                321
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    25  15
  20P LOSS WILD-TYPE 329 230
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                40                559 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                230 
$`20P LOSS MUTATED`
TCGA-L5-A43M TCGA-EQ-A4SO TCGA-2H-A9GI TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH 
        8.94        16.24        14.30        44.75        68.02        47.38 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NL TCGA-L5-A8NU TCGA-LN-A49M 
       26.33        32.61         3.32        13.22        83.24        12.66 
TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A7HW TCGA-LN-A7HY TCGA-R6-A6XG TCGA-S8-A6BW 
       13.41        12.46        12.00        12.03        38.40        20.38 
TCGA-VR-A8EQ TCGA-XP-A8T8 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-8289 
       22.82        14.37         6.18        17.29        26.10         2.66 
TCGA-BR-A4PD TCGA-CD-8525 TCGA-CG-4301 TCGA-D7-6519 TCGA-D7-8575 TCGA-D7-8576 
       20.65        12.59         3.02        20.55        18.21        14.66 
TCGA-EQ-5647 TCGA-HF-7133 TCGA-HU-8249 TCGA-IN-A6RJ TCGA-IN-AB1V TCGA-IP-7968 
        0.62        63.06        28.96        12.46        15.75         2.53 
TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PY TCGA-VQ-AA68 
        5.46        18.48        14.33        43.66 

$`20P LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF 
        0.23        20.15         9.86        27.35        26.93        25.78 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ 
       24.03         6.28         3.16        30.25         0.30        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        13.41        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R 
       10.36         5.92        10.45        12.43        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       10.52        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        27.09        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23         3.42         2.10         1.32         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         9.67         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51         0.46        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51        10.62        11.70        13.51         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        66.81        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        18.41        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.62               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             83.24             122.30 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            15.205             13.680 
[1] "0.6 - 83.2 (15.2)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         1        3        3        0         6         6
  20P LOSS WILD-TYPE       9       18       44       33        81        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           4          6          4          2        4
  20P LOSS WILD-TYPE        24         89         68         44       45
                    vv
clus                 STAGE IVA
  20P LOSS MUTATED           0
  20P LOSS WILD-TYPE         4
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  3                 18
  STAGE IB                  3                 44
  STAGE II                  0                 33
  STAGE IIA                 6                 81
  STAGE IIB                 6                 81
  STAGE III                 4                 24
  STAGE IIIA                6                 89
  STAGE IIIB                4                 68
  STAGE IIIC                2                 44
  STAGE IV                  4                 45
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20P LOSS MUTATED       6  10  19   6
  20P LOSS WILD-TYPE    49 126 264 118
D77V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                6                 49
  T2                  10                126
  T3                  19                264
  T4                   6                118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P LOSS MUTATED    14  13   8   6
  20P LOSS WILD-TYPE 193 174  90  90
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               14                193
  N1               13                174
  N2                8                 90
  N3                6                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    32   3
  20P LOSS WILD-TYPE 492  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     32    3
  20P LOSS WILD-TYPE  492   36
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               32                492
  1                3                 36
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    14  28
  20P LOSS WILD-TYPE 171 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     14   28
  20P LOSS WILD-TYPE  171  412
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               14                171
  MALE                 28                412
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    24  13
  20P LOSS WILD-TYPE 421 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     24   13
  20P LOSS WILD-TYPE  421  106
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                24                421
  YES               13                106
[1] 2 2
[1] FALSE
D77V9, continuous
D77V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED      10                         2
  20P LOSS WILD-TYPE   124                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           0    25
  20P LOSS WILD-TYPE                                         1   367
D77V11, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                                   10                124
  BLACK OR AFRICAN AMERICAN                                2                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   25                367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  23
  20P LOSS WILD-TYPE  10 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   23
  20P LOSS WILD-TYPE   10  381
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               23                381
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     6   2
  20Q LOSS WILD-TYPE 348 243
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                591 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                243 
$`20Q LOSS MUTATED`
TCGA-L5-A43M TCGA-JY-A6FA TCGA-JY-A6FH TCGA-LN-A7HW TCGA-LN-A9FR TCGA-S8-A6BW 
        8.94        44.75        47.38        12.00        12.26        20.38 
TCGA-VR-A8EQ TCGA-IN-A6RJ 
       22.82        12.46 

$`20Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       16.24         0.23        20.15         9.86        27.35        26.93 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       12.16       122.10        68.02         3.68        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        27.09        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       19.73        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              8.94               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             47.38             122.30 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             16.42              13.94 
[1] "8.9 - 47.4 (16.4)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.9"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         0        1        1        0         1         3
  20Q LOSS WILD-TYPE      10       20       46       33        86        84
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           1          0          0          0        0
  20Q LOSS WILD-TYPE        27         95         72         46       49
                    vv
clus                 STAGE IVA
  20Q LOSS MUTATED           0
  20Q LOSS WILD-TYPE         4
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 20
  STAGE IB                  1                 46
  STAGE II                  0                 33
  STAGE IIA                 1                 86
  STAGE IIB                 3                 84
  STAGE III                 1                 27
  STAGE IIIA                0                 95
  STAGE IIIB                0                 72
  STAGE IIIC                0                 46
  STAGE IV                  0                 49
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20Q LOSS MUTATED       1   5   2   0
  20Q LOSS WILD-TYPE    54 131 281 124
D78V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                1                 54
  T2                   5                131
  T3                   2                281
  T4                   0                124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q LOSS MUTATED     3   4   1   0
  20Q LOSS WILD-TYPE 204 183  97  96
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                3                204
  N1                4                183
  N2                1                 97
  N3                0                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   0
  20Q LOSS WILD-TYPE 518  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    0
  20Q LOSS WILD-TYPE  518   39
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                6                518
  1                0                 39
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   7
  20Q LOSS WILD-TYPE 184 433
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    7
  20Q LOSS WILD-TYPE  184  433
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                184
  MALE                  7                433
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6   2
  20Q LOSS WILD-TYPE 439 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6    2
  20Q LOSS WILD-TYPE  439  117
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 6                439
  YES                2                117
[1] 2 2
[1] FALSE
D78V9, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 66 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HX         TCGA-LN-A7HY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8ET         TCGA-VR-A8EU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7B         TCGA-VR-AA7D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-XP-A8T6         TCGA-XP-A8T7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D78V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20Q LOSS MUTATED       3                         0
  20Q LOSS WILD-TYPE   131                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q LOSS MUTATED                                           0     4
  20Q LOSS WILD-TYPE                                         1   388
D78V11, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                                    3                131
  BLACK OR AFRICAN AMERICAN                                0                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                388
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   4
  20Q LOSS WILD-TYPE  11 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    4
  20Q LOSS WILD-TYPE   11  400
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                4                400
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   163 115
  21Q LOSS WILD-TYPE 191 130
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               278                321 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               115                130 
$`21Q LOSS MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       18.28         4.31         8.94        24.00         4.70         0.36 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G 
       27.12         5.16        47.05        22.98         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL 
        9.86        27.35        26.93        25.78         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       13.94         8.94        32.45        33.27         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS 
       20.12        18.64         3.88         0.53         0.79         9.96 
TCGA-JY-A6F8 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
      122.10        23.18        31.56        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
        0.30        32.61        21.01        47.93         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         7.40         3.75         3.02         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
       16.47        13.55        13.22         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.85        10.36         5.92        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.38        13.15        13.25        12.76        12.85        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.22        12.33        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.33        13.38        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASW 
        9.30         2.89         2.30        12.69        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
        8.98        25.81        22.82        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        18.18        52.27        46.19        11.24         9.17 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
       41.23        14.37         2.10         2.66        19.73        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 
       11.01         9.44         6.97        18.35         4.08         9.67 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 
       13.68        19.33        26.10         9.17        31.20        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
       33.63        39.78        28.73        33.21        14.43        11.44 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        9.60         8.05        19.96        15.58         7.40        31.10 
TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 
       17.52         4.31        14.04        14.79         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 
        9.21        24.79         9.86        20.88        10.68         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       34.98         1.48         0.72        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       20.42         1.15        21.44        12.76        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.33        12.39        12.82        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4466 
       12.20        20.02        54.08         4.01        12.03        18.97 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
       30.97         6.97         1.02        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6525 TCGA-D7-6526 
        4.01        69.04        20.91        19.13        13.35        17.19 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU 
       15.98        12.79        11.31        14.66        21.14        16.44 
TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C 
       11.31        15.65        19.96         0.62        72.23        11.38 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 
       19.53        17.06         6.21        63.06        26.47         1.51 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4GU 
       28.96        22.82        22.68         3.25         8.98         6.58 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 
        0.26        29.00        23.84        23.80        21.17        36.36 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR 
       18.81         3.39        18.38        12.46        13.35         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        11.70        15.75         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        37.64        36.95        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8MV TCGA-RD-A8MW 
        8.52        74.53         6.08         9.24       122.30        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
      115.69        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       48.79        13.25        18.48         7.73        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91K 
        1.87        23.41        64.57        14.33        39.45        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A91Z 
       18.74        20.81         1.71        42.64         9.73        55.56 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        2.01        55.43         4.54        21.04        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6J 
       18.41        43.66        32.94        17.13        54.12        27.55 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`21Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        60.39        34.85        19.99        22.82        35.97 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-2H-A9GH TCGA-2H-A9GI 
       20.02        21.99        79.07        16.24        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YB 
       58.55        16.24         4.21         7.69        35.21         2.63 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
        9.30        17.03        23.41        12.82        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4ON 
       47.38        21.70        25.22         6.28        26.33        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM 
        3.32         1.38        25.12        55.50        13.48         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49P 
        5.49        21.37        83.24        10.45        12.66        12.33 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        12.62        12.46        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59        22.39        15.52        11.54         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-R6-A6L4 TCGA-R6-A6Y0 
       10.52        13.18         0.13        12.03        16.31        53.95 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       15.78         7.00        20.38         5.29         3.42        15.35 
TCGA-VR-A8EP TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR 
       27.09        18.31        33.70        18.05        15.91        18.21 
TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI 
       25.08         3.42         1.32        58.03        26.70        19.56 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        9.47         6.61         4.64         7.43        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.87        17.29        39.12        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        30.90        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       21.90         9.21        36.16        35.84        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 
        3.45         9.07        29.56        37.25         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 
       32.25         0.56        29.42         2.66         2.20         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 
       13.08         0.26        22.19         0.95        26.33         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
       11.80        31.27         7.36        25.05         3.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T 
        7.53        26.73        31.96        32.58         8.22        34.13 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       13.87         6.08        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL 
       14.17         0.53        28.34         0.66        32.52        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       11.21        12.10        12.59        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG 
       15.39        12.07        12.43         6.31        12.30         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
        7.99         8.05        14.01        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
        9.01         7.07        12.00        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
        0.99       105.07        28.96        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       10.26        15.22        12.36        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       19.50        17.19        18.21        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
       20.32        22.29         8.38         4.34         7.13         7.99 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       14.47        21.27         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7134 
        5.03        13.58         0.56         5.52        77.29        52.21 
TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       30.51         5.92        24.39        18.15        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD 
        0.76        24.30         5.59        24.26        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       20.25         2.10        12.95        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-AB1X TCGA-MX-A5UG 
        3.45        19.53         6.44        12.59        13.51         3.72 
TCGA-MX-A5UJ TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       19.73         4.60        11.05         8.61         5.13        16.67 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DU 
       40.64       116.38        71.38        16.87        19.04         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ 
        2.70         9.27        15.65        13.35        29.59        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 
       11.70        21.83        32.88        60.85         9.50         9.04 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6A 
        6.58         5.72        66.81         2.66        28.41        38.93 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        17.26 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.23               0.00 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            122.30             116.38 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             13.30              14.86 
[1] "0.2 - 122.3 (13.3)" "0.0 - 116.4 (14.9)"
[1] "hr=" "1"  
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         7        8       22       10        38        37
  21Q LOSS WILD-TYPE       3       13       25       23        49        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED          18         48         32         20       19
  21Q LOSS WILD-TYPE        10         47         40         26       30
                    vv
clus                 STAGE IVA
  21Q LOSS MUTATED           2
  21Q LOSS WILD-TYPE         2
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   7                  3
  STAGE IA                  8                 13
  STAGE IB                 22                 25
  STAGE II                 10                 23
  STAGE IIA                38                 49
  STAGE IIB                37                 50
  STAGE III                18                 10
  STAGE IIIA               48                 47
  STAGE IIIB               32                 40
  STAGE IIIC               20                 26
  STAGE IV                 19                 30
  STAGE IVA                 2                  2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  21Q LOSS MUTATED      25  59 136  48
  21Q LOSS WILD-TYPE    30  77 147  76
D79V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               25                 30
  T2                  59                 77
  T3                 136                147
  T4                  48                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q LOSS MUTATED    88  89  47  41
  21Q LOSS WILD-TYPE 119  98  51  55
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               88                119
  N1               89                 98
  N2               47                 51
  N3               41                 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"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   238  14
  21Q LOSS WILD-TYPE 286  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    238   14
  21Q LOSS WILD-TYPE  286   25
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              238                286
  1               14                 25
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    87 200
  21Q LOSS WILD-TYPE  98 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     87  200
  21Q LOSS WILD-TYPE   98  240
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               87                 98
  MALE                200                240
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   198  61
  21Q LOSS WILD-TYPE 247  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    198   61
  21Q LOSS WILD-TYPE  247   58
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO               198                247
  YES               61                 58
[1] 2 2
[1] FALSE
D79V9, continuous
D79V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED      53                         8
  21Q LOSS WILD-TYPE    81                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           0   183
  21Q LOSS WILD-TYPE                                         1   209
D79V11, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                                   53                 81
  BLACK OR AFRICAN AMERICAN                                8                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  183                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"
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     6 166
  21Q LOSS WILD-TYPE   5 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6  166
  21Q LOSS WILD-TYPE    5  238
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  5
  NOT HISPANIC OR LATINO              166                238
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   118  94
  22Q LOSS WILD-TYPE 236 151
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               212                387 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                94                151 
$`22Q LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-CG-4444 
       34.85        18.28        24.00         4.70         0.36        47.05 
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       21.99        16.24        20.15         9.86        27.35        26.93 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YB 
       13.94         8.94        16.24         4.21        32.45         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 
       18.64         3.88         0.53         0.79        23.41         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OS 
      122.10        47.38        31.56         3.16        32.61        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
        4.90        29.00         7.13         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        5.49         8.71        46.09        10.36         5.92        10.45 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 
       13.41        13.38        15.35        13.25        12.62        12.76 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       10.52        12.03        13.18         8.02         7.59         5.06 
TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
       38.40        15.78         2.89         7.00         5.29        16.44 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-XP-A8T8 TCGA-Z6-A8JE 
        9.27        25.81        22.82        18.31        14.37         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        2.66        19.73        58.03        11.01         9.44         6.61 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 
        4.08         9.67         6.18        17.29        19.33        26.10 
TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-8058 
        9.17        12.16         9.21        33.63        39.78        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8369 
       14.43        11.44         0.69         9.60         7.40        14.04 
TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
       25.18        26.73        24.79        32.58         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF 
       10.68        34.98         0.72        32.52        20.65         1.15 
TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       21.44        13.15        13.35        12.76        12.53         7.17 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.39        15.39        12.07         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.43        11.61        12.20         8.05        54.08         4.01 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 
       18.97        30.97        12.03        15.02        69.04        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 
       20.91        20.55        10.26        15.22        12.79        11.31 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 
       19.50        18.21        21.14        16.44        11.31        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF 
       19.96         0.62        19.53        17.06         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP 
        6.21        63.06         5.92        28.96        22.75         8.98 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 
        0.26         2.10        23.84        21.17        33.40         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU 
       18.38        12.46        19.53         6.44         6.74        11.70 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 
       15.75         2.53         5.56        36.95        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 
       18.21         6.08         8.61        16.67       115.69        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       18.48        46.26        22.19        12.79        17.85         1.87 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       14.33        39.45        18.74        20.81         1.71        42.64 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A 
        9.50         9.73        66.81        11.24        18.41        38.93 
TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       32.94         0.79 

$`22Q LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         4.31         8.94        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4475 TCGA-CG-5727 
       35.97        27.12         5.16        20.02        22.98        79.07 
TCGA-FP-A8CX TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        0.23         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       20.12         9.30        17.03        12.82         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        23.18        25.22        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        7.17         1.38         3.16         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       25.12         3.75         7.76        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S 
       52.57        10.85        12.66        12.43        12.33        13.15 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.59        12.46        12.59        12.49        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.33        25.25        12.00        12.23        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.82        16.31         7.04         6.35        53.95         9.30 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX 
        2.30        12.69        20.38         3.42        15.35         8.98 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       27.09        12.43         1.55         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       15.91        18.21        25.08        41.23         3.42         1.32 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 
        7.43        18.35        30.90         4.08         9.34         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        44.94        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       35.84        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       29.56        33.21        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
       29.42         2.66        19.96         2.20        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        7.53        31.96        20.88        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
       20.42        16.14         5.13        13.41        13.02        13.18 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       11.21        12.10        12.59        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.64        12.82        12.43         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        12.00         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        28.96        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       21.07         7.99        25.71        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 
       18.61        17.85        13.35        17.19        15.98        12.36 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 
       12.33        24.72        16.80        17.19        14.66        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.24        11.44        20.32        22.29         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        14.07        22.29        59.54         5.03        13.58 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       77.29        52.21        30.51        26.47         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       18.15        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        24.26        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
       20.25        12.95        29.00        23.80        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NR 
       36.36         3.45        18.81        13.35        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
       10.62        13.51        63.62        37.64         3.72        19.73 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52        74.53         4.60         9.24        11.05         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        8.94        16.87        19.04        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       38.14        37.22         7.73        30.97        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.50         2.70         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       29.59        64.57        73.41        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       32.88        60.85        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        21.04         2.66        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        28.41        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.26               0.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             122.1              122.3 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             13.25              14.50 
[1] "0.3 - 122.1 (13.2)" "0.0 - 122.3 (14.5)"
[1] "hr=" "1.2"
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         6        2       18       12        26        29
  22Q LOSS WILD-TYPE       4       19       29       21        61        58
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED          18         35         26         13       16
  22Q LOSS WILD-TYPE        10         60         46         33       33
                    vv
clus                 STAGE IVA
  22Q LOSS MUTATED           3
  22Q LOSS WILD-TYPE         1
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   6                  4
  STAGE IA                  2                 19
  STAGE IB                 18                 29
  STAGE II                 12                 21
  STAGE IIA                26                 61
  STAGE IIB                29                 58
  STAGE III                18                 10
  STAGE IIIA               35                 60
  STAGE IIIB               26                 46
  STAGE IIIC               13                 33
  STAGE IV                 16                 33
  STAGE IVA                 3                  1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  22Q LOSS MUTATED      22  42 112  33
  22Q LOSS WILD-TYPE    33  94 171  91
D80V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1               22                 33
  T2                  42                 94
  T3                 112                171
  T4                  33                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q LOSS MUTATED    63  70  37  34
  22Q LOSS WILD-TYPE 144 117  61  62
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               63                144
  N1               70                117
  N2               37                 61
  N3               34                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   185  12
  22Q LOSS WILD-TYPE 339  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    185   12
  22Q LOSS WILD-TYPE  339   27
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              185                339
  1               12                 27
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    59 159
  22Q LOSS WILD-TYPE 126 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     59  159
  22Q LOSS WILD-TYPE  126  281
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               59                126
  MALE                159                281
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   150  51
  22Q LOSS WILD-TYPE 295  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    150   51
  22Q LOSS WILD-TYPE  295   68
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               150                295
  YES               51                 68
[1] 2 2
[1] FALSE
D80V9, continuous
D80V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED      42                         4
  22Q LOSS WILD-TYPE    92                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           1   137
  22Q LOSS WILD-TYPE                                         0   255
D80V11, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                                   42                 92
  BLACK OR AFRICAN AMERICAN                                4                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  137                255
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     4 130
  22Q LOSS WILD-TYPE   7 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4  130
  22Q LOSS WILD-TYPE    7  274
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO              130                274
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    77  44
  XP LOSS WILD-TYPE 277 201
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              121               478 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               44               201 
$`XP LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-S8-A6BV TCGA-CG-4444 TCGA-VQ-A8PU 
       34.85        18.28        24.00        20.02        47.05        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
       26.93        25.78        14.30         4.21        32.45        35.21 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         3.88         0.53        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OJ 
        4.67        44.75        47.38        23.18        30.25        21.01 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NR 
       18.35         7.17         3.75        13.48        16.47         8.71 
TCGA-L5-A8NS TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49R 
       13.41        46.09         5.92        12.66        12.33        13.38 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.46        12.59        22.39        13.22        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN 
       12.00        13.38         0.13        12.26        33.11         8.02 
TCGA-R6-A6KZ TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        5.06         2.30        12.69        16.44         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-XP-A8T8 
       25.81        18.31         8.12        52.27        15.91        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 
        3.42         2.10        58.03        19.56         9.44        18.35 
TCGA-BR-6458 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8680 
       19.33        19.96         7.40        31.10        13.08        31.96 
TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 
        9.86        13.87        34.98         1.15        21.44        12.76 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 
       11.64        12.07        12.82        11.31        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-CG-5734 
        3.02        29.98        19.07         7.07        15.02         7.99 
TCGA-D7-5579 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 
       20.91        15.22        15.98        12.79        12.33        18.21 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-FP-8211 
       11.31        20.32        22.29        15.65        19.96        13.58 
TCGA-FP-A4BF TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8663 
        5.52        22.82        22.75        23.80        36.36         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-KB-A93J TCGA-R5-A7O7 
       18.38        13.35         6.44         6.74        36.95        45.67 
TCGA-VQ-A8PC TCGA-VQ-A8PS TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6A 
       46.26        13.35        55.56        66.81        43.66        38.93 
TCGA-VQ-AA6D 
       17.13 

$`XP LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39         4.31         8.94         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4460 
       22.82         0.36        35.97        27.12         5.16        21.99 
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
       16.24         7.69        33.27         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A7DP TCGA-IG-A97H 
       18.64         9.30        17.03         0.79        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       12.16       122.10        68.02         3.68        41.52        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       26.33        32.61        47.93         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N 
       83.24        52.57        10.85        10.36        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33         4.47        12.33        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.33        13.18        12.03        12.85         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89         7.00        20.38         5.29         3.42 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX 
       15.35        27.09        22.82        12.43         1.55        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        46.19        18.05        11.24         9.17 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.21        25.08        41.23         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       32.25         8.05         0.56        29.42         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       15.58         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       20.88         8.22        10.68        34.13         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
       12.59        15.39        12.43         6.31        12.30        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 
       11.61         6.58        11.77        12.62        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4477 
       12.03         0.00         9.01        18.97        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07        25.71        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM 
       22.29        17.06        59.54         5.03         0.56         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
        5.92        24.39        18.15        28.96        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS 
       33.40         3.45        18.81        12.46        19.53        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        37.64         3.72        19.73        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.13              0.00 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            66.81            122.30 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           15.220            13.615 
[1] "0.1 - 66.8 (15.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         3        2       10        5        20        19
  XP LOSS WILD-TYPE       7       19       37       28        67        68
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           8         24         11          7        5
  XP LOSS WILD-TYPE        20         71         61         39       44
                   vv
clus                STAGE IVA
  XP LOSS MUTATED           0
  XP LOSS WILD-TYPE         4
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  3                 7
  STAGE IA                 2                19
  STAGE IB                10                37
  STAGE II                 5                28
  STAGE IIA               20                67
  STAGE IIB               19                68
  STAGE III                8                20
  STAGE IIIA              24                71
  STAGE IIIB              11                61
  STAGE IIIC               7                39
  STAGE IV                 5                44
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XP LOSS MUTATED      10  30  59  17
  XP LOSS WILD-TYPE    45 106 224 107
D81V4, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  T0+T1              10                45
  T2                 30               106
  T3                 59               224
  T4                 17               107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XP LOSS MUTATED    44  41  21   9
  XP LOSS WILD-TYPE 163 146  77  87
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              44               163
  N1              41               146
  N2              21                77
  N3               9                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   105   4
  XP LOSS WILD-TYPE 419  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    105    4
  XP LOSS WILD-TYPE  419   35
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0             105               419
  1               4                35
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    20 103
  XP LOSS WILD-TYPE 165 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     20  103
  XP LOSS WILD-TYPE  165  337
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              20               165
  MALE               103               337
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    83  25
  XP LOSS WILD-TYPE 362  94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     83   25
  XP LOSS WILD-TYPE  362   94
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               83               362
  YES              25                94
[1] 2 2
[1] FALSE
D81V9, continuous
D81V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XP LOSS MUTATED      31                         1
  XP LOSS WILD-TYPE   103                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP LOSS MUTATED                                           0    76
  XP LOSS WILD-TYPE                                         1   316
D81V11, multiclass
                                           clus
vv                                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                                  31               103
  BLACK OR AFRICAN AMERICAN                               1                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  76               316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     4  75
  XP LOSS WILD-TYPE   7 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      4   75
  XP LOSS WILD-TYPE    7  329
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 7
  NOT HISPANIC OR LATINO              75               329
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    60  37
  XQ LOSS WILD-TYPE 294 208
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               97               502 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               37               208 
$`XQ LOSS MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-CG-4444 TCGA-VQ-A8PU TCGA-VQ-A94U 
       34.85        18.28        24.00        47.05        27.35        26.93 
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A625 TCGA-JY-A6FH TCGA-L5-A43E 
       25.78         4.21        32.45        12.82        47.38        30.25 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A891 TCGA-L5-A8NI 
       21.01        18.35         7.17         3.16         3.75        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L5-A8NW TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49Y 
       16.47         8.71        46.09        12.33        13.38        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.59        22.39        13.22        25.25        10.52        12.00 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC 
       33.11         8.02         5.06         2.30        12.69         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8Q7 
       16.44         9.27         8.98        25.81         8.12        52.27 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 
        3.42         2.10        58.03        19.56         9.44        18.35 
TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8678 TCGA-BR-8680 
       19.33         9.21        19.96        31.10        24.79        31.96 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 
       13.87        34.98         1.48         1.15        21.44        12.76 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 
       11.64        12.07        12.82        11.31        20.02         3.02 
TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-5579 
        7.99        29.98        19.07         7.07        15.02        20.91 
TCGA-D7-6519 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX 
       20.55        12.79        12.33        18.21        14.66        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A74A TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7133 
       20.32        22.29        19.96        13.58         5.52        63.06 
TCGA-HU-8604 TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RP 
       22.82        23.80        36.36         3.39        18.38         6.44 
TCGA-IN-A6RR TCGA-KB-A93J TCGA-VQ-A8E0 TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-AA6A 
        6.74        36.95        18.48        13.35        20.81        38.93 
TCGA-VQ-AA6D 
       17.13 

$`XQ LOSS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39         4.31         8.94         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
        9.86        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       13.94         8.94        16.24         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       32.61        47.93         3.32         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK 
        7.40         3.02        55.50         2.66        12.92        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.62        12.49        12.76        12.59        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY 
       11.54        12.33         4.47        12.33        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.85        12.26         7.82         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ 
        7.00        20.38         5.29        15.35        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31        28.11        33.70        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08        41.23        14.37         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 
        9.34        28.14         6.28         7.53        26.73        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 
        9.86        20.88         8.22        10.68        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        6.08        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
       12.59        15.39        12.43         6.31        12.30        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
       11.61         6.58        12.20        11.77        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4477 
       12.03         0.00         9.01        18.97        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        25.71        12.66        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.22        15.98        12.36        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        17.19        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       11.44        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        0.56         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ 
       14.07        15.68        33.40         3.45        18.81        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       13.35        19.53        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       15.75        13.51         2.53         5.56        63.62        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        28.41        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             1.15              0.00 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            63.06            122.30 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            16.44             13.73 
[1] "1.1 - 63.1 (16.4)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D82V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         3        3        9        6        14        11
  XQ LOSS WILD-TYPE       7       18       38       27        73        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           6         18          7          5        5
  XQ LOSS WILD-TYPE        22         77         65         41       44
                   vv
clus                STAGE IVA
  XQ LOSS MUTATED           0
  XQ LOSS WILD-TYPE         4
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  3                 7
  STAGE IA                 3                18
  STAGE IB                 9                38
  STAGE II                 6                27
  STAGE IIA               14                73
  STAGE IIB               11                76
  STAGE III                6                22
  STAGE IIIA              18                77
  STAGE IIIB               7                65
  STAGE IIIC               5                41
  STAGE IV                 5                44
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XQ LOSS MUTATED       9  22  47  12
  XQ LOSS WILD-TYPE    46 114 236 112
D82V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1               9                46
  T2                 22               114
  T3                 47               236
  T4                 12               112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ LOSS MUTATED    35  28  16  10
  XQ LOSS WILD-TYPE 172 159  82  86
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              35               172
  N1              28               159
  N2              16                82
  N3              10                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    82   2
  XQ LOSS WILD-TYPE 442  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     82    2
  XQ LOSS WILD-TYPE  442   37
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              82               442
  1               2                37
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    17  81
  XQ LOSS WILD-TYPE 168 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     17   81
  XQ LOSS WILD-TYPE  168  359
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              17               168
  MALE                81               359
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    64  22
  XQ LOSS WILD-TYPE 381  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     64   22
  XQ LOSS WILD-TYPE  381   97
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               64               381
  YES              22                97
[1] 2 2
[1] FALSE
D82V9, continuous
D82V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED      19                         2
  XQ LOSS WILD-TYPE   115                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           0    61
  XQ LOSS WILD-TYPE                                         1   331
D82V11, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                                  19               115
  BLACK OR AFRICAN AMERICAN                               2                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  61               331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  58
  XQ LOSS WILD-TYPE   9 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   58
  XQ LOSS WILD-TYPE    9  346
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              58               346
[1] 2 2
[1] FALSE
